Package {WebGestaltR}

Type: Package
Title: Gene Set Analysis Toolkit WebGestaltR
Version: 1.0.0
Date: 2026-07-29
Description: The web version WebGestalt https://www.webgestalt.org supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
License: LGPL-2 | LGPL-2.1 | LGPL-3 [expanded from: LGPL]
URL: https://github.com/bzhanglab/WebGestaltR, https://bzhanglab.github.io/WebGestaltR/
LazyLoad: yes
Depends: R (≥ 4.0)
Imports: methods, dplyr, doRNG, readr, parallel (≥ 3.3.2), doParallel (≥ 1.0.10), foreach (≥ 1.4.0), jsonlite, httr, rlang, svglite, whisker, apcluster, Rcpp, cluster, poolr
NeedsCompilation: yes
LinkingTo: Rcpp
RoxygenNote: 7.3.2
SystemRequirements: Cargo (Rust's package manager), rustc v1.63.0+
Config/rextendr/version: 0.4.2
Config/WebGestaltR/MSRV: 1.63.0
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Packaged: 2026-07-30 14:22:33 UTC; shiz
Author: John Elizarraras [aut], Jing Wang [aut], Yuxing Liao [aut], Eric Jaehnig [ctb], Zhiao Shi [aut, cre], Quanhu Sheng [ctb]
Maintainer: Zhiao Shi <zhiao.shi@gmail.com>
Repository: CRAN
Date/Publication: 2026-07-30 23:20:22 UTC

WebGestaltR: The R interface for enrichment analysis with WebGestalt.

Description

The web version WebGestalt https://www.webgestalt.org supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.

Main function for enrichment analysis

Usage

WebGestaltR(
  enrichMethod = "ORA",
  organism = "hsapiens",
  enrichDatabase = NULL,
  enrichDatabaseFile = NULL,
  enrichDatabaseType = NULL,
  enrichDatabaseDescriptionFile = NULL,
  interestGeneFile = NULL,
  interestGene = NULL,
  interestGeneType = NULL,
  interestGeneNames = NULL,
  collapseMethod = "mean",
  referenceGeneFile = NULL,
  referenceGene = NULL,
  referenceGeneType = NULL,
  referenceSet = NULL,
  minNum = 10,
  maxNum = 500,
  sigMethod = "fdr",
  fdrMethod = "BH",
  fdrThr = 0.05,
  topThr = 10,
  reportNum = 20,
  perNum = 1000,
  gseaP = 1,
  isOutput = TRUE,
  outputDirectory = getwd(),
  projectName = NULL,
  dagColor = "continuous",
  saveRawGseaResult = FALSE,
  gseaPlotFormat = c("png", "svg"),
  setCoverNum = 10,
  networkConstructionMethod = NULL,
  neighborNum = 10,
  highlightType = "Seeds",
  highlightSeedNum = 10,
  nThreads = 1,
  cache = NULL,
  hostName = "https://www.webgestalt.org/",
  useWeightedSetCover = FALSE,
  useAffinityPropagation = FALSE,
  usekMedoid = TRUE,
  kMedoid_k = 25,
  listName = NULL,
  ...
)

WebGestaltRBatch(
  interestGeneFolder = NULL,
  enrichMethod = "ORA",
  isParallel = FALSE,
  nThreads = 3,
  ...
)

Arguments

enrichMethod

Enrichment methods: ORA, GSEA or NTA.

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

enrichDatabase

The functional categories for the enrichment analysis. Users can use the function listGeneSet to check the available functional databases for the selected organism. Multiple databases in a vector are supported for ORA and GSEA.

enrichDatabaseFile

Users can provide one or more GMT files as the functional category for enrichment analysis. The extension of the file should be gmt and the first column of the file is the category ID, the second one is the external link for the category. Genes annotated to the category are from the third column. All columns are separated by tabs. The GMT files will be combined with enrichDatabase.

enrichDatabaseType

The ID type of the genes in the enrichDatabaseFile. If users set organism as others, users do not need to set this ID type because WebGestaltR will not perform ID mapping for other organisms. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType.

enrichDatabaseDescriptionFile

Users can also provide description files for the custom enrichDatabaseFile. The extension of the description file should be des. The description file contains two columns: the first column is the category ID that should be exactly the same as the category ID in the custom enrichDatabaseFile and the second column is the description of the category. All columns are separated by tabs.

interestGeneFile

If enrichMethod is ORA or NTA, the extension of the interestGeneFile should be txt and the file can only contain one column: the interesting gene list. If enrichMethod is GSEA, the extension of the interestGeneFile should be rnk and the file should contain two columns separated by tab: the gene list and the corresponding scores.

interestGene

Users can also use an R object as the input. If enrichMethod is ORA or NTA, interestGene should be an R vector object containing the interesting gene list. If enrichMethod is GSEA, interestGene should be an R data.frame object containing two columns: the gene list and the corresponding scores.

interestGeneType

The ID type of the interesting gene list. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType. If the organism is others, users do not need to set this parameter.

interestGeneNames

The names of the id lists for multiomics data.

collapseMethod

The method to collapse duplicate IDs with scores. mean, median, min and max represent the mean, median, minimum and maximum of scores for the duplicate IDs.

referenceGeneFile

For the ORA method, the users need to upload the reference gene list. The extension of the referenceGeneFile should be txt and the file can only contain one column: the reference gene list.

referenceGene

For the ORA method, users can also use an R object as the reference gene list. referenceGene should be an R vector object containing the reference gene list.

referenceGeneType

The ID type of the reference gene list. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType. If the organism is others, users do not need to set this parameter.

referenceSet

Users can directly select the reference set from existing platforms in WebGestaltR and do not need to provide the reference set through referenceGeneFile. All existing platforms supported in WebGestaltR can be found by the function listReferenceSet. If referenceGeneFile and refereneceGene are NULL, WebGestaltR will use the referenceSet as the reference gene set. Otherwise, WebGestaltR will use the user supplied reference set for enrichment analysis.

minNum

WebGestaltR will exclude the categories with the number of annotated genes less than minNum for enrichment analysis. The default is 10.

maxNum

WebGestaltR will exclude the categories with the number of annotated genes larger than maxNum for enrichment analysis. The default is 500.

sigMethod

Two methods of significance are available in WebGestaltR: fdr and top. fdr means the enriched categories are identified based on the FDR and top means all categories are ranked based on FDR and then select top categories as the enriched categories. The default is fdr.

fdrMethod

For the ORA method, WebGestaltR supports five FDR methods: holm, hochberg, hommel, bonferroni, BH and BY. The default is BH.

fdrThr

The significant threshold for the fdr method. The default is 0.05.

topThr

The threshold for the top method. The default is 10.

reportNum

The number of enriched categories visualized in the final report. The default is 20. A larger reportNum may be slow to render in the report.

perNum

The number of permutations for the GSEA method. The default is 1000.

gseaP

The exponential scaling factor of the phenotype score. The default is 1. When p=0, ES reduces to standard K-S statistics (See original paper for more details).

isOutput

If isOutput is TRUE, WebGestaltR will create a folder named by the projectName and save the results in the folder. Otherwise, WebGestaltR will only return an R data.frame object containing the enrichment results. If hundreds of gene list need to be analyzed simultaneously, it is better to set isOutput to FALSE. The default is TRUE.

outputDirectory

The output directory for the results.

projectName

The name of the project. If projectName is NULL, WebGestaltR will use time stamp as the project name.

dagColor

If dagColor is binary, the significant terms in the DAG structure will be colored by steel blue for ORA method or steel blue (positive related) and dark orange (negative related) for GSEA method. If dagColor is continous, the significant terms in the DAG structure will be colored by the color gradient based on corresponding FDRs.

saveRawGseaResult

Whether the raw result from GSEA is saved as a RDS file, which can be used for plotting. Defaults to FALSE. The list includes

Enrichment_Results

A data frame of GSEA results with statistics

Running_Sums

A matrix of running sum of scores for each gene set

Items_in_Set

A list with ranks of genes for each gene set

gseaPlotFormat

The graphic format of GSEA enrichment plots. Either svg, png, or c("png", "svg") (default).

setCoverNum

The number of expected gene sets after set cover to reduce redundancy. It could get fewer sets if the coverage reaches 100%. The default is 10.

networkConstructionMethod

Netowrk construction method for NTA. Either Network_Retrieval_Prioritization or Network_Expansion. Network Retrieval & Prioritization first uses random walk analysis to calculate random walk probabilities for the input seeds, then identifies the relationships among the seeds in the selected network and returns a retrieval sub-network. The seeds with the top random walk probabilities are highlighted in the sub-network. Network Expansion first uses random walk analysis to rank all genes in the selected network based on their network proximity to the input seeds and then return an expanded sub-network in which nodes are the input seeds and their top ranking neighbors and edges represent their relationships.

neighborNum

The number of neighbors to include in NTA Network Expansion method.

highlightType

The type of nodes to highlight in the NTA Network Expansion method, either Seeds or Neighbors.

highlightSeedNum

The number of top input seeds to highlight in NTA Network Retrieval & Prioritizaiton method.

nThreads

The number of cores to use for GSEA and set cover, and in batch function.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

hostName

The server URL for accessing data. Mostly for development purposes.

useWeightedSetCover

Use weighted set cover for ORA. Defaults to TRUE.

useAffinityPropagation

Use affinity propagation for ORA. Defaults to FALSE.

usekMedoid

Use k-medoid for ORA. Defaults to TRUE.

kMedoid_k

The number of clusters for k-medoid. Defaults to 25.

listName

(optional) The names of the analyte list. Used to give the HTML title of the report. Defaults to NULL.

...

In batch function, passes parameters to WebGestaltR function. Also handles backward compatibility for some parameters in old versions.

interestGeneFolder

Run WebGestaltR for gene list files in the folder.

isParallel

If jobs are run parallelly in the batch.

Details

WebGestaltR function can perform three enrichment analyses: ORA (Over-Representation Analysis) and GSEA (Gene Set Enrichment Analysis).and NTA (Network Topology Analysis). Based on the user-uploaded gene list or gene list with scores, WebGestaltR function will first map the gene list to the entrez gene ids and then summarize the gene list based on the GO (Gene Ontology) Slim. After performing the enrichment analysis, WebGestaltR function also returns a user-friendly HTML report containing GO Slim summary and the enrichment analysis result. If functional categories have DAG (directed acyclic graph) structure or genes in the functional categories have network structure, those relationship can also be visualized in the report.

Value

The WebGestaltR function returns a data frame containing the enrichment analysis result and also outputs an user-friendly HTML report if isOutput is TRUE. The columns in the data frame depend on the enrichMethod and they are the following:

geneSet

ID of the gene set.

description

Description of the gene set if available.

link

Link to the data source.

size

The number of genes in the set after filtering by minNum and maxNum.

overlap

The number of mapped input genes that are annotated in the gene set.

expect

Expected number of input genes that are annotated in the gene set.

enrichmentRatio

Enrichment ratio, overlap / expect.

enrichmentScore

Enrichment score, the maximum running sum of scores for the ranked list.

normalizedEnrichmentScore

Normalized enrichment score, normalized against the average enrichment score of all permutations.

leadingEdgeNum

Number of genes/phosphosites in the leading edge.

pValue

P-value from hypergeometric test for ORA. For GSEA, please refer to its original publication or online at https://docs.gsea-msigdb.org/#GSEA/GSEA_User_Guide/.

FDR

Corrected P-value for mulilple testing with fdrMethod for ORA.

overlapId

The gene/phosphosite IDs of overlap for ORA (entrez gene IDs or phosphosite sequence).

leadingEdgeId

Genes/phosphosites in the leading edge in entrez gene ID or phosphosite sequence.

userId

The gene/phosphosite IDs of overlap for ORA or leadingEdgeId for GSEA in User input IDs.

plotPath

Path of the GSEA enrichment plot.

database

Name of the source database if multiple enrichment databases are given.

goId

In NTA, like geneSet, the enriched GO terms of genes in the returned subnetwork.

interestGene

In NTA, the gene IDs in the subnetwork with 0/1 annotations indicating if it is from user input.

The WebGestaltRBatch function returns a list of enrichment results.

Author(s)

Maintainer: John Elizarraras john.elizarraras@bcm.edu

Authors:

Other contributors:

See Also

Useful links:

Examples

## Not run: 
####### ORA example #########
geneFile <- system.file("extdata", "interestingGenes.txt", package = "WebGestaltR")
refFile <- system.file("extdata", "referenceGenes.txt", package = "WebGestaltR")
outputDirectory <- getwd()
enrichResult <- WebGestaltR(
  enrichMethod = "ORA", organism = "hsapiens",
  enrichDatabase = "pathway_KEGG", interestGeneFile = geneFile,
  interestGeneType = "genesymbol", referenceGeneFile = refFile,
  referenceGeneType = "genesymbol", isOutput = TRUE,
  outputDirectory = outputDirectory, projectName = NULL
)

####### GSEA example #########
rankFile <- system.file("extdata", "GeneRankList.rnk", package = "WebGestaltR")
outputDirectory <- getwd()
enrichResult <- WebGestaltR(
  enrichMethod = "GSEA", organism = "hsapiens",
  enrichDatabase = "pathway_KEGG", interestGeneFile = rankFile,
  interestGeneType = "genesymbol", sigMethod = "top", topThr = 10, minNum = 5,
  outputDirectory = outputDirectory
)

####### NTA example #########
enrichResult <- WebGestaltR(
  enrichMethod = "NTA", organism = "hsapiens",
  enrichDatabase = "network_PPI_BIOGRID", interestGeneFile = geneFile,
  interestGeneType = "genesymbol", sigMethod = "top", topThr = 10,
  outputDirectory = getwd(), highlightSeedNum = 10,
  networkConstructionMethod = "Network_Retrieval_Prioritization"
)

## End(Not run)

WebGestaltRMultiOmics

Description

Perform multi-omics analysis using WebGestaltR

Usage

WebGestaltRMultiOmics(
  analyteLists = NULL,
  analyteListFiles = NULL,
  analyteTypes = NULL,
  enrichMethod = "ORA",
  organism = "hsapiens",
  enrichDatabase = NULL,
  enrichDatabaseFile = NULL,
  enrichDatabaseType = NULL,
  enrichDatabaseDescriptionFile = NULL,
  collapseMethod = "mean",
  minNum = 10,
  maxNum = 500,
  fdrMethod = "BH",
  sigMethod = "fdr",
  fdrThr = 0.05,
  topThr = 10,
  reportNum = 100,
  setCoverNum = 10,
  perNum = 1000,
  gseaP = 1,
  isOutput = TRUE,
  outputDirectory = getwd(),
  projectName = NULL,
  dagColor = "binary",
  saveRawGseaResult = FALSE,
  gseaPlotFormat = "png",
  nThreads = 1,
  cache = NULL,
  hostName = "https://www.webgestalt.org/",
  useWeightedSetCover = TRUE,
  useAffinityPropagation = FALSE,
  usekMedoid = FALSE,
  kMedoid_k = 25,
  isMetaAnalysis = TRUE,
  mergeMethod = "mean",
  normalizationMethod = "rank",
  referenceLists = NULL,
  referenceListFiles = NULL,
  referenceTypes = NULL,
  referenceSets = NULL,
  listNames = NULL
)

Arguments

analyteLists

vector of the ID type of the corresponding interesting analyte list. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType. If the organism is others, users do not need to set this parameter. The length of analyteLists should be the same as the length of analyteListFiles or analyteLists.

analyteListFiles

If enrichMethod is ORA, the extension of the analyteListFiles should be txt and each file can only contain one column: the interesting analyte list. If enrichMethod is GSEA, the extension of the analyteListFiles should be rnk and the files should contain two columns separated by tab: the analyte list and the corresponding scores.

analyteTypes

a vector containing the ID types of the analyte lists.

enrichMethod

Enrichment methods: ORAor GSEA.

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

enrichDatabase

The functional categories for the enrichment analysis. Users can use the function listGeneSet to check the available functional databases for the selected organism. Multiple databases in a vector are supported for ORA and GSEA.

enrichDatabaseFile

Users can provide one or more GMT files as the functional category for enrichment analysis. The extension of the file should be gmt and the first column of the file is the category ID, the second one is the external link for the category. Genes annotated to the category are from the third column. All columns are separated by tabs. The GMT files will be combined with enrichDatabase.

enrichDatabaseType

The ID type of the genes in the enrichDatabaseFile. If users set organism as others, users do not need to set this ID type because WebGestaltR will not perform ID mapping for other organisms. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType.

enrichDatabaseDescriptionFile

Users can also provide description files for the custom enrichDatabaseFile. The extension of the description file should be des. The description file contains two columns: the first column is the category ID that should be exactly the same as the category ID in the custom enrichDatabaseFile and the second column is the description of the category. All columns are separated by tabs.

collapseMethod

The method to collapse duplicate IDs with scores. mean, median, min and max represent the mean, median, minimum and maximum of scores for the duplicate IDs.

minNum

WebGestaltR will exclude the categories with the number of annotated genes less than minNum for enrichment analysis. The default is 10.

maxNum

WebGestaltR will exclude the categories with the number of annotated genes larger than maxNum for enrichment analysis. The default is 500.

fdrMethod

For the ORA method, WebGestaltR supports five FDR methods: holm, hochberg, hommel, bonferroni, BH and BY. The default is BH.

sigMethod

Two methods of significance are available in WebGestaltR: fdr and top. fdr means the enriched categories are identified based on the FDR and top means all categories are ranked based on FDR and then select top categories as the enriched categories. The default is fdr.

fdrThr

The significant threshold for the fdr method. The default is 0.05.

topThr

The threshold for the top method. The default is 10.

reportNum

The number of enriched categories visualized in the final report. The default is 20. A larger reportNum may be slow to render in the report.

setCoverNum

The number of expected gene sets after set cover to reduce redundancy. It could get fewer sets if the coverage reaches 100%. The default is 10.

perNum

The number of permutations for the GSEA method. The default is 1000.

gseaP

The exponential scaling factor of the phenotype score. The default is 1. When p=0, ES reduces to standard K-S statistics (See original paper for more details).

isOutput

If isOutput is TRUE, WebGestaltR will create a folder named by the projectName and save the results in the folder. Otherwise, WebGestaltR will only return an R data.frame object containing the enrichment results. If hundreds of gene list need to be analyzed simultaneously, it is better to set isOutput to FALSE. The default is TRUE.

outputDirectory

The output directory for the results.

projectName

The name of the project. If projectName is NULL, WebGestaltR will use time stamp as the project name.

dagColor

If dagColor is binary, the significant terms in the DAG structure will be colored by steel blue for ORA method or steel blue (positive related) and dark orange (negative related) for GSEA method. If dagColor is continous, the significant terms in the DAG structure will be colored by the color gradient based on corresponding FDRs.

saveRawGseaResult

Whether the raw result from GSEA is saved as a RDS file, which can be used for plotting. Defaults to FALSE. The list includes

Enrichment_Results

A data frame of GSEA results with statistics

Running_Sums

A matrix of running sum of scores for each gene set

Items_in_Set

A list with ranks of genes for each gene set

gseaPlotFormat

The graphic format of GSEA enrichment plots. Either svg, png, or c("png", "svg") (default).

nThreads

The number of cores to use for GSEA and set cover, and in batch function.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

hostName

The server URL for accessing data. Mostly for development purposes.

useWeightedSetCover

Use weighted set cover for ORA. Defaults to TRUE.

useAffinityPropagation

Use affinity propagation for ORA. Defaults to FALSE.

usekMedoid

Use k-medoid for ORA. Defaults to TRUE.

kMedoid_k

The number of clusters for k-medoid. Defaults to 25.

isMetaAnalysis

whether to perform meta-analysis. Defaults to TRUE. FALSE is not currently implemented.

mergeMethod

The method to merge the results from multiple omics (options: mean, max). Only used if isMetaAnalysis = FALSE. Defaults to mean.

normalizationMethod

The method to normalize the results from multiple omics (options: rank, median, mean). Only used if isMetaAnalysis = FALSE.

referenceLists

For the ORA method, users can also use an R object as the reference gene list. referenceLists should be an R vector object containing the reference gene list.

referenceListFiles

For the ORA method, the users need to upload the reference gene list. The extension of the referenceListFile should be txt and the file can only contain one column: the reference gene list.

referenceTypes

Vector of the ID types of the reference lists. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType. If the organism is others, users do not need to set this parameter.

referenceSets

Users can directly select the reference sets from existing platforms in WebGestaltR and do not need to provide the reference set through referenceListFiles. All existing platforms supported in WebGestaltR can be found by the function listReferenceSets. If referenceListFiles and refereneceLists are NULL, WebGestaltR will use the referenceSets as the reference analyte sets. Otherwise, WebGestaltR will use the user supplied reference set for enrichment analysis. Must be a vector with length matching the input analyte list (i.e. c('genome', 'genome', 'KEGG'))

listNames

The names of the analyte lists.

Multi-omics GSEA importFrom dplyr bind_rows left_join arrange select desc importFrom readr write_tsv

Description

Multi-omics GSEA importFrom dplyr bind_rows left_join arrange select desc importFrom readr write_tsv

Usage

WebGestaltRMultiOmicsGSEA(
  analyteLists = NULL,
  analyteListFiles = NULL,
  analyteTypes = NULL,
  enrichMethod = "GSEA",
  organism = "hsapiens",
  enrichDatabase = NULL,
  enrichDatabaseFile = NULL,
  enrichDatabaseType = NULL,
  enrichDatabaseDescriptionFile = NULL,
  collapseMethod = "mean",
  minNum = 10,
  maxNum = 500,
  fdrMethod = "BH",
  sigMethod = "fdr",
  fdrThr = 0.05,
  topThr = 10,
  reportNum = 100,
  setCoverNum = 10,
  perNum = 1000,
  gseaP = 1,
  isOutput = TRUE,
  outputDirectory = getwd(),
  projectName = NULL,
  dagColor = "binary",
  saveRawGseaResult = FALSE,
  gseaPlotFormat = "png",
  nThreads = 1,
  cache = NULL,
  hostName = "https://www.webgestalt.org/",
  useWeightedSetCover = TRUE,
  useAffinityPropagation = FALSE,
  usekMedoid = FALSE,
  kMedoid_k = 25,
  isMetaAnalysis = TRUE,
  mergeMethod = "mean",
  normalizationMethod = "rank",
  listNames = NULL
)

Arguments

analyteLists

vector of the ID type of the corresponding interesting analyte list. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType. If the organism is others, users do not need to set this parameter. The length of analyteLists should be the same as the length of analyteListFiles or analyteLists.

analyteListFiles

If enrichMethod is ORA, the extension of the analyteListFiles should be txt and each file can only contain one column: the interesting analyte list. If enrichMethod is GSEA, the extension of the analyteListFiles should be rnk and the files should contain two columns separated by tab: the analyte list and the corresponding scores.

analyteTypes

a vector containing the ID types of the analyte lists.

enrichMethod

Enrichment methods: ORAor GSEA.

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

enrichDatabase

The functional categories for the enrichment analysis. Users can use the function listGeneSet to check the available functional databases for the selected organism. Multiple databases in a vector are supported for ORA and GSEA.

enrichDatabaseFile

Users can provide one or more GMT files as the functional category for enrichment analysis. The extension of the file should be gmt and the first column of the file is the category ID, the second one is the external link for the category. Genes annotated to the category are from the third column. All columns are separated by tabs. The GMT files will be combined with enrichDatabase.

enrichDatabaseType

The ID type of the genes in the enrichDatabaseFile. If users set organism as others, users do not need to set this ID type because WebGestaltR will not perform ID mapping for other organisms. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType.

enrichDatabaseDescriptionFile

Users can also provide description files for the custom enrichDatabaseFile. The extension of the description file should be des. The description file contains two columns: the first column is the category ID that should be exactly the same as the category ID in the custom enrichDatabaseFile and the second column is the description of the category. All columns are separated by tabs.

collapseMethod

The method to collapse duplicate IDs with scores. mean, median, min and max represent the mean, median, minimum and maximum of scores for the duplicate IDs.

minNum

WebGestaltR will exclude the categories with the number of annotated genes less than minNum for enrichment analysis. The default is 10.

maxNum

WebGestaltR will exclude the categories with the number of annotated genes larger than maxNum for enrichment analysis. The default is 500.

fdrMethod

For the ORA method, WebGestaltR supports five FDR methods: holm, hochberg, hommel, bonferroni, BH and BY. The default is BH.

sigMethod

Two methods of significance are available in WebGestaltR: fdr and top. fdr means the enriched categories are identified based on the FDR and top means all categories are ranked based on FDR and then select top categories as the enriched categories. The default is fdr.

fdrThr

The significant threshold for the fdr method. The default is 0.05.

topThr

The threshold for the top method. The default is 10.

reportNum

The number of enriched categories visualized in the final report. The default is 20. A larger reportNum may be slow to render in the report.

setCoverNum

The number of expected gene sets after set cover to reduce redundancy. It could get fewer sets if the coverage reaches 100%. The default is 10.

perNum

The number of permutations for the GSEA method. The default is 1000.

gseaP

The exponential scaling factor of the phenotype score. The default is 1. When p=0, ES reduces to standard K-S statistics (See original paper for more details).

isOutput

If isOutput is TRUE, WebGestaltR will create a folder named by the projectName and save the results in the folder. Otherwise, WebGestaltR will only return an R data.frame object containing the enrichment results. If hundreds of gene list need to be analyzed simultaneously, it is better to set isOutput to FALSE. The default is TRUE.

outputDirectory

The output directory for the results.

projectName

The name of the project. If projectName is NULL, WebGestaltR will use time stamp as the project name.

dagColor

If dagColor is binary, the significant terms in the DAG structure will be colored by steel blue for ORA method or steel blue (positive related) and dark orange (negative related) for GSEA method. If dagColor is continous, the significant terms in the DAG structure will be colored by the color gradient based on corresponding FDRs.

saveRawGseaResult

Whether the raw result from GSEA is saved as a RDS file, which can be used for plotting. Defaults to FALSE. The list includes

Enrichment_Results

A data frame of GSEA results with statistics

Running_Sums

A matrix of running sum of scores for each gene set

Items_in_Set

A list with ranks of genes for each gene set

gseaPlotFormat

The graphic format of GSEA enrichment plots. Either svg, png, or c("png", "svg") (default).

nThreads

The number of cores to use for GSEA and set cover, and in batch function.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

hostName

The server URL for accessing data. Mostly for development purposes.

useWeightedSetCover

Use weighted set cover for ORA. Defaults to TRUE.

useAffinityPropagation

Use affinity propagation for ORA. Defaults to FALSE.

usekMedoid

Use k-medoid for ORA. Defaults to TRUE.

kMedoid_k

The number of clusters for k-medoid. Defaults to 25.

isMetaAnalysis

whether to perform meta-analysis. Defaults to TRUE. FALSE is not currently implemented.

mergeMethod

The method to merge the results from multiple omics (options: mean, max). Only used if isMetaAnalysis = FALSE. Defaults to mean.

normalizationMethod

The method to normalize the results from multiple omics (options: rank, median, mean). Only used if isMetaAnalysis = FALSE.

listNames

The names of the analyte lists.

Multi-omics ORA importFrom dplyr bind_rows left_join arrange select desc importFrom readr write_tsv

Description

Multi-omics ORA importFrom dplyr bind_rows left_join arrange select desc importFrom readr write_tsv

Usage

WebGestaltRMultiOmicsOra(
  analyteLists = NULL,
  analyteListFiles = NULL,
  analyteTypes = NULL,
  enrichMethod = "ORA",
  organism = "hsapiens",
  enrichDatabase = NULL,
  enrichDatabaseFile = NULL,
  enrichDatabaseType = NULL,
  enrichDatabaseDescriptionFile = NULL,
  collapseMethod = "mean",
  minNum = 10,
  maxNum = 500,
  fdrMethod = "BH",
  sigMethod = "fdr",
  fdrThr = 0.05,
  topThr = 10,
  reportNum = 100,
  setCoverNum = 10,
  perNum = 1000,
  gseaP = 1,
  isOutput = TRUE,
  outputDirectory = getwd(),
  projectName = NULL,
  dagColor = "binary",
  nThreads = 1,
  cache = NULL,
  hostName = "https://www.webgestalt.org/",
  useWeightedSetCover = TRUE,
  useAffinityPropagation = FALSE,
  usekMedoid = FALSE,
  kMedoid_k = 25,
  referenceLists = NULL,
  referenceListFiles = NULL,
  referenceTypes = NULL,
  referenceSets = NULL,
  listNames = NULL
)

Arguments

analyteLists

vector of the ID type of the corresponding interesting analyte list. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType. If the organism is others, users do not need to set this parameter. The length of analyteLists should be the same as the length of analyteListFiles or analyteLists.

analyteListFiles

If enrichMethod is ORA, the extension of the analyteListFiles should be txt and each file can only contain one column: the interesting analyte list. If enrichMethod is GSEA, the extension of the analyteListFiles should be rnk and the files should contain two columns separated by tab: the analyte list and the corresponding scores.

analyteTypes

a vector containing the ID types of the analyte lists.

enrichMethod

Enrichment methods: ORAor GSEA.

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

enrichDatabase

The functional categories for the enrichment analysis. Users can use the function listGeneSet to check the available functional databases for the selected organism. Multiple databases in a vector are supported for ORA and GSEA.

enrichDatabaseFile

Users can provide one or more GMT files as the functional category for enrichment analysis. The extension of the file should be gmt and the first column of the file is the category ID, the second one is the external link for the category. Genes annotated to the category are from the third column. All columns are separated by tabs. The GMT files will be combined with enrichDatabase.

enrichDatabaseType

The ID type of the genes in the enrichDatabaseFile. If users set organism as others, users do not need to set this ID type because WebGestaltR will not perform ID mapping for other organisms. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType.

enrichDatabaseDescriptionFile

Users can also provide description files for the custom enrichDatabaseFile. The extension of the description file should be des. The description file contains two columns: the first column is the category ID that should be exactly the same as the category ID in the custom enrichDatabaseFile and the second column is the description of the category. All columns are separated by tabs.

collapseMethod

The method to collapse duplicate IDs with scores. mean, median, min and max represent the mean, median, minimum and maximum of scores for the duplicate IDs.

minNum

WebGestaltR will exclude the categories with the number of annotated genes less than minNum for enrichment analysis. The default is 10.

maxNum

WebGestaltR will exclude the categories with the number of annotated genes larger than maxNum for enrichment analysis. The default is 500.

fdrMethod

For the ORA method, WebGestaltR supports five FDR methods: holm, hochberg, hommel, bonferroni, BH and BY. The default is BH.

sigMethod

Two methods of significance are available in WebGestaltR: fdr and top. fdr means the enriched categories are identified based on the FDR and top means all categories are ranked based on FDR and then select top categories as the enriched categories. The default is fdr.

fdrThr

The significant threshold for the fdr method. The default is 0.05.

topThr

The threshold for the top method. The default is 10.

reportNum

The number of enriched categories visualized in the final report. The default is 20. A larger reportNum may be slow to render in the report.

setCoverNum

The number of expected gene sets after set cover to reduce redundancy. It could get fewer sets if the coverage reaches 100%. The default is 10.

perNum

The number of permutations for the GSEA method. The default is 1000.

gseaP

The exponential scaling factor of the phenotype score. The default is 1. When p=0, ES reduces to standard K-S statistics (See original paper for more details).

isOutput

If isOutput is TRUE, WebGestaltR will create a folder named by the projectName and save the results in the folder. Otherwise, WebGestaltR will only return an R data.frame object containing the enrichment results. If hundreds of gene list need to be analyzed simultaneously, it is better to set isOutput to FALSE. The default is TRUE.

outputDirectory

The output directory for the results.

projectName

The name of the project. If projectName is NULL, WebGestaltR will use time stamp as the project name.

dagColor

If dagColor is binary, the significant terms in the DAG structure will be colored by steel blue for ORA method or steel blue (positive related) and dark orange (negative related) for GSEA method. If dagColor is continous, the significant terms in the DAG structure will be colored by the color gradient based on corresponding FDRs.

nThreads

The number of cores to use for GSEA and set cover, and in batch function.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

hostName

The server URL for accessing data. Mostly for development purposes.

useWeightedSetCover

Use weighted set cover for ORA. Defaults to TRUE.

useAffinityPropagation

Use affinity propagation for ORA. Defaults to FALSE.

usekMedoid

Use k-medoid for ORA. Defaults to TRUE.

kMedoid_k

The number of clusters for k-medoid. Defaults to 25.

referenceLists

For the ORA method, users can also use an R object as the reference gene list. referenceLists should be an R vector object containing the reference gene list.

referenceListFiles

For the ORA method, the users need to upload the reference gene list. The extension of the referenceListFile should be txt and the file can only contain one column: the reference gene list.

referenceTypes

Vector of the ID types of the reference lists. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType. If the organism is others, users do not need to set this parameter.

referenceSets

Users can directly select the reference sets from existing platforms in WebGestaltR and do not need to provide the reference set through referenceListFiles. All existing platforms supported in WebGestaltR can be found by the function listReferenceSets. If referenceListFiles and refereneceLists are NULL, WebGestaltR will use the referenceSets as the reference analyte sets. Otherwise, WebGestaltR will use the user supplied reference set for enrichment analysis. Must be a vector with length matching the input analyte list (i.e. c('genome', 'genome', 'KEGG'))

listNames

The names of the analyte lists.

Affinity Propagation

Description

Use affinity propagation to cluster similar gene sets to reduce redundancy in report.

Usage

affinityPropagation(idsInSet, score)

Arguments

idsInSet

A list of set names and their member IDs.

score

A vector of addible scores with the same length used to assign input preference; higher score has larger weight, i.e. -logP.

Value

A list of clusters and representatives for each cluster.

clusters

A list of character vectors of set IDs in each cluster.

representatives

A character vector of representatives for each cluster.

Author(s)

Zhiao Shi, Yuxing Liao

cacheUrl

Description

Get data from a URL or cache and optionally save in cache for reuse

Usage

cacheUrl(dataUrl, cache = NULL, query = NULL)

Arguments

dataUrl

The URL of data

cache

The cache directory. Defaults to NULL and fetches data from server.

query

The list of queries passed on to httr methods

Value

response object from httr request

createMetaReport

Description

Generate HTML report for ORA and GSEA MetaAnalysis

Usage

createMetaReport(
  hostName = NULL,
  outputDirectory = NULL,
  organism = "hsapiens",
  projectName = NULL,
  enrichMethod = NULL,
  geneSet_list = NULL,
  geneSetDes_list = NULL,
  geneSetDag_list = NULL,
  geneSetNet_list = NULL,
  interestingGeneMap_list = NULL,
  referenceGeneList_list = NULL,
  enrichedSig_list = NULL,
  geneTables_list = NULL,
  clusters_list = NULL,
  background_list,
  enrichDatabase_list = NULL,
  enrichDatabaseFile_list = NULL,
  enrichDatabaseType_list = NULL,
  enrichDatabaseDescriptionFile_list = NULL,
  interestGeneFile_list = NULL,
  interestGene_list = NULL,
  interestGeneType_list = NULL,
  collapseMethod = "mean",
  referenceGeneFile_list = NULL,
  referenceGene_list = NULL,
  referenceGeneType_list = NULL,
  referenceSet_list = NULL,
  minNum = 10,
  maxNum = 500,
  fdrMethod = "BH",
  sigMethod = "fdr",
  fdrThr = 0.05,
  topThr = 10,
  reportNum = 20,
  perNum = 1000,
  p = 1,
  dagColor = "binary",
  listNames = NULL
)

createMetaSummaryReport

Description

Generate HTML report for ORA and GSEA

Usage

createMetaSummaryReport(
  hostName,
  outputDirectory,
  organism = "hsapiens",
  projectName,
  enrichMethod,
  geneSet,
  geneSetDes,
  geneSetDag,
  geneSetNet,
  interestingGeneMap,
  referenceGeneList,
  enrichedSig,
  geneTables,
  clusters,
  background,
  enrichDatabase = NULL,
  enrichDatabaseFile = NULL,
  enrichDatabaseType = NULL,
  enrichDatabaseDescriptionFile = NULL,
  interestGeneFile = NULL,
  interestGene = NULL,
  interestGeneType = NULL,
  collapseMethod = "mean",
  referenceGeneFile = NULL,
  referenceGene = NULL,
  referenceGeneType = NULL,
  referenceSet = NULL,
  minNum = 10,
  maxNum = 500,
  fdrMethod = "BH",
  sigMethod = "fdr",
  fdrThr = 0.05,
  topThr = 10,
  reportNum = 20,
  perNum = 1000,
  p = 1,
  dagColor = "binary",
  is_meta = TRUE,
  outputHtmlFile = NULL,
  listNames = NULL
)

Create HTML Report for NTA

Description

Create HTML Report for NTA

Usage

createNtaReport(
  networkName,
  method,
  sigMethod,
  fdrThr,
  topThr,
  highlightType,
  outputDirectory,
  projectDir,
  projectName,
  hostName,
  listName = listName
)

createReport

Description

Generate HTML report for ORA and GSEA

Usage

createReport(
  hostName,
  outputDirectory,
  organism = "hsapiens",
  projectName,
  enrichMethod,
  geneSet,
  geneSetDes,
  geneSetDag,
  geneSetNet,
  interestingGeneMap,
  referenceGeneList,
  enrichedSig,
  geneTables,
  clusters,
  background,
  enrichDatabase = NULL,
  enrichDatabaseFile = NULL,
  enrichDatabaseType = NULL,
  enrichDatabaseDescriptionFile = NULL,
  interestGeneFile = NULL,
  interestGene = NULL,
  interestGeneType = NULL,
  collapseMethod = "mean",
  referenceGeneFile = NULL,
  referenceGene = NULL,
  referenceGeneType = NULL,
  referenceSet = NULL,
  minNum = 10,
  maxNum = 500,
  fdrMethod = "BH",
  sigMethod = "fdr",
  fdrThr = 0.05,
  topThr = 10,
  reportNum = 20,
  perNum = 1000,
  p = 1,
  dagColor = "binary",
  is_meta = FALSE,
  outputHtmlFile = NULL,
  listName = NULL
)

enrichResultSection

Description

Conditionally render template of main result section. Actual work is carried out in front end

Usage

enrichResultSection(
  enrichMethod,
  enrichedSig,
  geneSet,
  geneSetDes,
  geneSetDag,
  geneSetNet,
  clusters
)

Expand enriched GO IDs to include ancestors up to the root

Description

Returns expanded nodes and DAG tree edges

Usage

expandDag(goTermList, dagEdgeList)

Fill relation data frame for GSEA input

Description

Fill 1 for gene in gene set

Usage

fill_input_data_frame(gmt, genes, gene_sets)

Arguments

gmt

A Data Frame with geneSet and gene columns from the GMT file

genes

A vector of genes

gene_sets

A vector of gene sets

Details

See https://github.com/extendr/extendr/issues/612 for how to export DataFrame

## Diagram “'shell Gene Sets First column named 'gene' containing gene name A0100110100 1 = in set Genes B0100101000 0 = not in set C1011101001 Due to limitiations with extendr-api v 0.6.0, function returns a list, and the R package will add the first 'gene' column “'

Value

A Data Frame with the first column of gene and 1 or 0 for other columns of gene sets.

Author(s)

John Elizarraras

Check Format and Read Data

Description

Check Format and Read Data

Usage

formatCheck(dataType = "list", inputGeneFile = NULL, inputGene = NULL)

Arguments

dataType

Type of data, either list, rnk or gmt. Could be list, rnk or matrix for idToSymbol.

inputGeneFile

The data file to be mapped.

inputGene

Or the input could be given as an R object. GMT file should be read with readGmt.

Value

A list of data frame

GO Slim Summary

Description

Outputs a brief summary of input genes based on GO Slim data.

Usage

goSlimSummary(
  organism = "hsapiens",
  geneList,
  outputFile,
  outputType = "pdf",
  isOutput = TRUE,
  cache = NULL,
  hostName = "https://www.webgestalt.org"
)

Arguments

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

geneList

A list of input genes.

outputFile

Output file name.

outputType

File format of the plot: pdf, bmp or png.

isOutput

Boolean if a plot is save to outputFile.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

hostName

The server URL for accessing data. Mostly for development purposes.

Value

A list of the summary result.

Run GSEA using rust library

Description

Run GSEA using rust library

Usage

gsea_rust(min_overlap, max_overlap, permutations, sets, parts, analytes, ranks)

Arguments

min_overlap

the minimum overlap between analyte set and analyte list

max_overlap

the maximum overlap between analyte set and analyte list

permutations

the number of permutations to run

sets

A vector of analyte set names

parts

A list of the analytse in the analyte sets

analytes

A vector of analytes names in the GSEA list

ranks

A vector of ranks for the analytes in the GSEA list

Value

List of the results of GSEA

Author(s)

John Elizarraras

ID Mapping

Description

ID mapping utility with WebGestalt server.

Usage

idMapping(
  organism = "hsapiens",
  dataType = "list",
  inputGeneFile = NULL,
  inputGene = NULL,
  sourceIdType,
  targetIdType = NULL,
  collapseMethod = "mean",
  mappingOutput = FALSE,
  outputFileName = "",
  cache = NULL,
  hostName = "https://www.webgestalt.org/"
)

idToSymbol(
  organism = "hsapiens",
  dataType = "list",
  inputGeneFile = NULL,
  inputGene = NULL,
  sourceIdType = "ensembl_gene_id",
  collapseMethod = "mean",
  mappingOutput = FALSE,
  outputFileName = NULL,
  cache = NULL,
  hostName = "https://www.webgestalt.org/"
)

Arguments

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

dataType

Type of data, either list, rnk or gmt. Could be list, rnk or matrix for idToSymbol.

inputGeneFile

The data file to be mapped.

inputGene

Or the input could be given as an R object. GMT file should be read with readGmt.

sourceIdType

The ID type of the data.

targetIdType

The ID type of the mapped data.

collapseMethod

The method to collapse duplicate IDs with scores. mean, median, min and max represent the mean, median, minimum and maximum of scores for the duplicate IDs.

mappingOutput

Boolean if the mapping output is written to file.

outputFileName

The output file name.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

hostName

The server URL for accessing data. Mostly for development purposes.

Value

A list of mapped and unmapped IDs.

Jaccard Similarity

Description

Calculate Jaccard Similarity.

Usage

jaccardSim(idsInSet, score)

Arguments

idsInSet

A list of set names and their member IDs.

score

A vector of addible scores with the same length used to assign input preference; higher score has larger weight, i.e. -logP.

Value

A list of similarity matrix sim.mat and input preference vector ip.vec.

Author(s)

Zhiao Shi, Yuxing Liao

kMedoid

Description

kMedoid clustering

Usage

kMedoid(idsInSet, score, maxK = 10)

Arguments

idsInSet

a list of sets of ids

score

a vector of scores for each set

maxK

maximum number of clusters

keepRep

Description

Add representatives of redundancy-reduced clusters to topResult if they are missing.

Usage

keepRep(topResult, allResult, reps)

Modify the link to highlight the genes in the pathways

Description

Currently, we only have wikipathway and kegg pathways that need to modify the link

Usage

linkModification(
  enrichMethod,
  enrichPathwayLink,
  geneList,
  interestingGeneMap,
  hostName = "https://www.webgestalt.org/"
)

List WebGestalt Servers

Description

List available WebGestalt servers.

Usage

listArchiveUrl()

Value

A data frame of available servers.

List Gene Sets

Description

List available gene sets for the given organism on WebGestalt server.

Usage

listGeneSet(
  organism = "hsapiens",
  hostName = "https://www.webgestalt.org/",
  cache = NULL
)

Arguments

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

hostName

The server URL for accessing data. Mostly for development purposes.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

Value

A data frame of available gene sets.

List ID Types

Description

List supported ID types for the given organism on WebGestalt server.

Usage

listIdType(
  organism = "hsapiens",
  hostName = "https://www.webgestalt.org/",
  cache = NULL
)

Arguments

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

hostName

The server URL for accessing data. Mostly for development purposes.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

Value

A list of supported gene sets.

List Organisms

Description

List supported organisms on WebGestalt server.

Usage

listOrganism(hostName = "https://www.webgestalt.org/", cache = NULL)

Arguments

hostName

The server URL for accessing data. Mostly for development purposes.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

Value

A list of supported organisms.

List Reference Sets

Description

List available reference sets for the given organism on WebGestalt server.

Usage

listReferenceSet(
  organism = "hsapiens",
  hostName = "https://www.webgestalt.org/",
  cache = NULL
)

Arguments

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

hostName

The server URL for accessing data. Mostly for development purposes.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

Value

A list of reference sets.

Load gene set data

Description

Load gene set data

Usage

loadGeneSet(
  organism = "hsapiens",
  enrichDatabase = NULL,
  enrichDatabaseFile = NULL,
  enrichDatabaseType = NULL,
  enrichDatabaseDescriptionFile = NULL,
  cache = NULL,
  hostName = "https://www.webgestalt.org/",
  isMultiOmics = FALSE
)

Arguments

organism

Currently, WebGestaltR supports 12 organisms. Users can use the function listOrganism to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

enrichDatabase

The functional categories for the enrichment analysis. Users can use the function listGeneSet to check the available functional databases for the selected organism. Multiple databases in a vector are supported for ORA and GSEA.

enrichDatabaseFile

Users can provide one or more GMT files as the functional category for enrichment analysis. The extension of the file should be gmt and the first column of the file is the category ID, the second one is the external link for the category. Genes annotated to the category are from the third column. All columns are separated by tabs. The GMT files will be combined with enrichDatabase.

enrichDatabaseType

The ID type of the genes in the enrichDatabaseFile. If users set organism as others, users do not need to set this ID type because WebGestaltR will not perform ID mapping for other organisms. The supported ID types of WebGestaltR for the selected organism can be found by the function listIdType.

enrichDatabaseDescriptionFile

Users can also provide description files for the custom enrichDatabaseFile. The extension of the description file should be des. The description file contains two columns: the first column is the category ID that should be exactly the same as the category ID in the custom enrichDatabaseFile and the second column is the description of the category. All columns are separated by tabs.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

hostName

The server URL for accessing data. Mostly for development purposes.

isMultiOmics

Boolean if loading gene sets for multiomics. Defaults to FALSE.

Value

A list of geneSet, geneSetDes, geneSetDag, geneSetNet, standardId.

geneSet

Gene set: A data frame with columns of "geneSet", "description", "genes"

geneSetDes

Description: A data frame with columns of two columns of gene set ID and description

geneSetDag

DAG: A edge list data frame of two columns of parent and child. Or a list of data frames if multilple databases are given.

geneSetNet

Network: A edge list data frame of two columns connecting nodes. Or a list of data frames if multilple databases are given.

standardId

The standard ID of the gene set

metaEnrichResultSection

Description

Conditionally render template of main result section. Actual work is carried out in front end

Usage

metaEnrichResultSection(
  enrichMethod,
  enrichedSig,
  geneSet,
  geneSetDes,
  geneSetDag,
  geneSetNet,
  clusters
)

Modify the link to highlight the genes in the pathways

Description

Currently, we only have wikipathway and kegg pathways that need to modify the link

Usage

metaLinkModification(
  enrichMethod,
  enrichPathwayLink,
  geneList,
  interestingGeneMap_list,
  hostName = "https://www.webgestalt.org/",
  geneSet
)

metaSummaryDescription

Description

Render job summary section

Usage

metaSummaryDescription(
  projectName,
  organism,
  interestGeneFile,
  interestGene,
  interestGeneType,
  enrichMethod,
  enrichDatabase,
  enrichDatabaseFile,
  enrichDatabaseType,
  enrichDatabaseDescriptionFile,
  interestingGeneMap,
  referenceGeneList,
  referenceGeneFile,
  referenceGene,
  referenceGeneType,
  referenceSet,
  minNum,
  maxNum,
  sigMethod,
  fdrThr,
  topThr,
  fdrMethod,
  enrichedSig,
  reportNum,
  perNum,
  p,
  geneSet,
  repAdded,
  numAnnoRefUserId,
  hostName,
  listNames
)

Site Weighted Gene Set Enrichment Analysis

Description

Performs site weighted gene set enrichment analysis or standard GSEA when likelihood/weight columns in input_df are 1 or 0, p=1, q=1 and thresh_type="val".

Usage

multiswGsea(
  input_df_list,
  thresh_type = "percentile",
  thresh = 0.9,
  thresh_action = "exclude",
  min_set_size = 10,
  max_set_size = 500,
  max_score = "max",
  min_score = "min",
  psuedocount = 0.001,
  perms = 1000,
  p = 1,
  q = 1,
  nThreads = 1,
  rng_seed = 1,
  fork = FALSE,
  fdrMethod = "BH"
)

Arguments

input_df_list

A data frame in which first column is name of item of interest (gene, protein, phosphosite, etc.), the second is the correlation of that item of interest with the phenotype (typically log ratio of expression for phenotype vs. normal), and the remaining columns are the scores for the likelihood that the item belongs in each set (one column per set).

thresh_type

The type of thresh. Use 'percentile' to include all scores over that percentile given in thresh (i.e., 0.9 would be all items in 90th percentile, or top 10 percent); 'list' to include a list of set lists where the set lists are in the same order as the corresponding set columns in the input_df; 'val' to apply a single threshold value to all sets; or 'values' to use a vector of unique cutoffs for each set (needs to be in the same order as the sets are specified in the columns of input_df")

thresh

Depends on thresh_type. A list of lists of the items in each set (with same names as colnames of the scores); a numeric vector of threshold scores for each set (in the same order as the colnames of the scores in the input_df), or a single percentile value between 0 and 1 (i.e., if thresh=0.9, the 90th percentile of the score or the highest scoring 10 of of the items are included in the set for each scoring regimen) (thresh ="all" is not supported at this time, as it doesn't result in a Kolgorov-Smirnoff statistic; this may be worked in as an alternate scoring method later on).

thresh_action

Either "include", "exclude (default)", or "adjust"; this specifies how to treat each set if it doesn't contain a minimum number of items or contains all of the items; this option cannot be used with predefined lists of items in sets (if the number of items in a given set doesn't meet requirements, that set will be skipped).

min_set_size, max_set_size

The minimum/maximum number of items each set needs for the analysis to proceed.

max_score, min_score

A optional numeric vector of minimum/maximum boundaries to clip scores for each set.

psuedocount

Psuedocount (pc) is used for rescaling set scores: (score - min_score + pc)/(max_score - min_score +pc); this is needed to prevent division by 0 if max_score==min_score (in this case, all scores for items in set will be 1, which is equivalent to standard GSEA); it also allows users to adjust weights for scores that are close to the minimum for the scores in the set (unless min_score==max_score): as psuedocount value approaches 0, scaled minimum scores also approach 0; as psuedocount approaches infinity, scaled minimum scores approach the scaled maximum scores (which equal 1); this value must be larger than 0.

perms

The number of permutations.

p

The exponential scaling factor of the phenotype score (second column in input_df).

q

The exponential scaling factor of the likelihood score (weights).

nThreads

The number of threads to use in calculating permutaions.

rng_seed

Random seed.

fork

A boolean. Whether pass "fork" to type parameter of makeCluster on Unix-like machines.

fdrMethod

For the ORA method, WebGestaltR supports five FDR methods: holm, hochberg, hommel, bonferroni, BH and BY. The default is BH.

Details

The formula for weighting is as follows

\frac{s_{j}^{q}|r_{j}|^{p}}{\sum s^{q}|r|^{p}}

Where r is log ratio score, s is likelihood score, j is the index of the gene.

Value

A list of Enrichment_Results, Items_in_Set and Running_Sums.

Enrichment_Results

A data frame with row names of gene set and columns of "ES", "NES", "p_val", "fdr".

Items_in_Set

A list of one-column data frames. Describes genes and their ranks in each set.

Running_Sums

Running sum scores along genes sorted by ranked scores, with gene sets as columns.

Author(s)

John Elizarraras

Calculate random walk permutations for a network from seeds

Description

Calculate random walk permutations for a network from seeds

Usage

nta_rust(edge_list, seeds)

Arguments

edge_list

A list of edges

seeds

A list of seeds

Value

A list of nodes and scores

Author(s)

John Elizarraras

Run ORA using Rust library

Description

Run ORA using Rust library

Usage

ora_rust(sets, parts, interest, reference)

Arguments

sets

A vector of analyte set names

parts

A list of the analyte in the analyte sets

interest

A vector of analytes of interest

reference

A vector of analytes in the reference set

Value

A list of the results of ORA

Author(s)

John Elizarraras

Prepare input for standard GSEA

Description

A helper to read files for performing standard GSEA.

Usage

prepareGseaInput(rankFile, gmtFile)

Arguments

rankFile

Path of the rnk file

gmtFile

Path of the GMT file

Value

a data frame to be used in swGsea

Prepare Input Matrix for GSEA

Description

Prepare Input Matrix for GSEA

Usage

prepareInputMatrixGsea(rank, gmt)

Arguments

rank

A 2 column Data Frame of gene and score

gmt

3 column Data Frame of geneSet, description, and gene

Value

A matrix used for input to swGsea.

Read GMT File

Description

Read GMT File

Usage

readGmt(gmtFile, cache = NULL)

Arguments

gmtFile

The file path or URL of the GMT file.

cache

A directory to save data cache for reuse. Defaults to NULL and disabled.

Value

A data frame with columns of "geneSet", "description", "gene".

Run multiomics ORA using Rust library

Description

Run multiomics ORA using Rust library

Usage

rust_multiomics_ora(sets, big_part_vec, interest, reference, method)

Arguments

sets

list of the names of the analyte sets

big_part_vec

list of the analyte in the analyte sets

interest

list of analytes of interest

reference

list of analytes in the reference set

method

meta-analysis method to get meta-p values

Value

A list of vectors containing the results of ORA, with each list corresponding to each input list

Author(s)

John Elizarraras

specificParameterSummaryGsea

Description

Render job summary section of GSEA specific parameters

Usage

specificParameterSummaryGsea(
  organism,
  interestingGeneMap,
  geneSet,
  minNum,
  maxNum,
  sigMethod,
  fdrThr,
  topThr,
  perNum,
  p,
  enrichedSig,
  reportNum,
  repAdded
)

specificParameterSummaryOra

Description

Render job summary section of ORA specific parameters

Usage

specificParameterSummaryOra(
  organism,
  referenceGeneList,
  geneSet,
  referenceGeneFile,
  referenceGene,
  referenceGeneType,
  referenceSet,
  minNum,
  maxNum,
  sigMethod,
  fdrThr,
  topThr,
  fdrMethod,
  enrichedSig,
  reportNum,
  repAdded,
  numAnnoRefUserId,
  interestingGeneMap,
  hostName
)

summaryDescription

Description

Render job summary section

Usage

summaryDescription(
  projectName,
  organism,
  interestGeneFile,
  interestGene,
  interestGeneType,
  enrichMethod,
  enrichDatabase,
  enrichDatabaseFile,
  enrichDatabaseType,
  enrichDatabaseDescriptionFile,
  interestingGeneMap,
  referenceGeneList,
  referenceGeneFile,
  referenceGene,
  referenceGeneType,
  referenceSet,
  minNum,
  maxNum,
  sigMethod,
  fdrThr,
  topThr,
  fdrMethod,
  enrichedSig,
  reportNum,
  perNum,
  p,
  geneSet,
  repAdded,
  numAnnoRefUserId,
  hostName
)

Site Weighted Gene Set Enrichment Analysis

Description

Performs site weighted gene set enrichment analysis or standard GSEA when likelihood/weight columns in input_df are 1 or 0, p=1, q=1 and thresh_type="val".

Usage

swGsea(
  input_df,
  thresh_type = "percentile",
  thresh = 0.9,
  thresh_action = "exclude",
  min_set_size = 10,
  max_set_size = 500,
  max_score = "max",
  min_score = "min",
  psuedocount = 0.001,
  perms = 1000,
  p = 1,
  q = 1,
  nThreads = 1,
  rng_seed = 1,
  fork = FALSE
)

Arguments

input_df

A data frame in which first column is name of item of interest (gene, protein, phosphosite, etc.), the second is the correlation of that item of interest with the phenotype (typically log ratio of expression for phenotype vs. normal), and the remaining columns are the scores for the likelihood that the item belongs in each set (one column per set).

thresh_type

The type of thresh. Use 'percentile' to include all scores over that percentile given in thresh (i.e., 0.9 would be all items in 90th percentile, or top 10 percent); 'list' to include a list of set lists where the set lists are in the same order as the corresponding set columns in the input_df; 'val' to apply a single threshold value to all sets; or 'values' to use a vector of unique cutoffs for each set (needs to be in the same order as the sets are specified in the columns of input_df")

thresh

Depends on thresh_type. A list of lists of the items in each set (with same names as colnames of the scores); a numeric vector of threshold scores for each set (in the same order as the colnames of the scores in the input_df), or a single percentile value between 0 and 1 (i.e., if thresh=0.9, the 90th percentile of the score or the highest scoring 10 of of the items are included in the set for each scoring regimen) (thresh ="all" is not supported at this time, as it doesn't result in a Kolgorov-Smirnoff statistic; this may be worked in as an alternate scoring method later on).

thresh_action

Either "include", "exclude (default)", or "adjust"; this specifies how to treat each set if it doesn't contain a minimum number of items or contains all of the items; this option cannot be used with predefined lists of items in sets (if the number of items in a given set doesn't meet requirements, that set will be skipped).

min_set_size, max_set_size

The minimum/maximum number of items each set needs for the analysis to proceed.

max_score, min_score

A optional numeric vector of minimum/maximum boundaries to clip scores for each set.

psuedocount

Psuedocount (pc) is used for rescaling set scores: (score - min_score + pc)/(max_score - min_score +pc); this is needed to prevent division by 0 if max_score==min_score (in this case, all scores for items in set will be 1, which is equivalent to standard GSEA); it also allows users to adjust weights for scores that are close to the minimum for the scores in the set (unless min_score==max_score): as psuedocount value approaches 0, scaled minimum scores also approach 0; as psuedocount approaches infinity, scaled minimum scores approach the scaled maximum scores (which equal 1); this value must be larger than 0.

perms

The number of permutations.

p

The exponential scaling factor of the phenotype score (second column in input_df).

q

The exponential scaling factor of the likelihood score (weights).

nThreads

The number of threads to use in calculating permutaions.

rng_seed

Random seed.

fork

A boolean. Whether pass "fork" to type parameter of makeCluster on Unix-like machines.

Details

The formula for weighting is as follows

\frac{s_{j}^{q}|r_{j}|^{p}}{\sum s^{q}|r|^{p}}

Where r is log ratio score, s is likelihood score, j is the index of the gene.

Value

A list of Enrichment_Results, Items_in_Set and Running_Sums.

Enrichment_Results

A data frame with row names of gene set and columns of "ES", "NES", "p_val", "fdr".

Items_in_Set

A list of one-column data frames. Describes genes and their ranks in each set.

Running_Sums

Running sum scores along genes sorted by ranked scores, with gene sets as columns.

Author(s)

Eric Jaehnig

Weighted Set Cover

Description

Size constrained weighted set cover problem to find top N sets while maximizing the coverage of all elements.

Usage

weightedSetCover(idsInSet, costs, topN, nThreads = 4)

Arguments

idsInSet

A list of set names and their member IDs.

costs

A vector of the same length to add weights for penalty, i.e. 1/-logP.

topN

The number of sets (or less when it completes early) to return.

nThreads

The number of processes to use. In Windows, it fallbacks to 1.

Value

A list of topSets and coverage.

topSets

A list of set IDs.

coverage

The percentage of IDs covered in the top sets.

Author(s)

Zhiao Shi, Yuxing Liao