slideimp: Numeric Matrices K-NN and PCA Imputation
Fast k-nearest neighbors (K-NN) and principal component
analysis (PCA) imputation algorithms for missing values in epigenetic
data or other high-dimensional numeric matrices. For PCA, a locally
optimal block preconditioned conjugate gradient (LOBPCG) eigensolver
with warm starts of both the eigenblock and search direction is also
supported. Two complementary imputation strategies are available.
Group-wise imputation (e.g., by chromosome) is recommended for
Illumina DNA methylation microarrays (e.g., 450K, EPIC) and other
matrices with groupable columns. A sliding window approach for K-NN or
PCA imputation is recommended only for whole-genome methylation data
such as whole-genome bisulfite sequencing (WGBS) or Enzymatic
Methyl-seq (EM-seq). The package also supports hyperparameter tuning
via repeated cross-validation. The K-NN algorithm is described in:
Hastie, T., Tibshirani, R., Sherlock, G., Eisen, M., Brown, P. and
Botstein, D. (1999) "Imputing Missing Data for Gene Expression
Arrays". The PCA imputation is an optimized reimplementation of the
imputePCA() function from the 'missMDA' package described in: Josse,
J. and Husson, F. (2016) <doi:10.18637/jss.v070.i01> "missMDA: A
Package for Handling Missing Values in Multivariate Data Analysis".
| Version: |
1.2.0 |
| Depends: |
R (≥ 4.3.0) |
| Imports: |
bigmemory, checkmate, cli, collapse, mirai, Rcpp, stats, utils |
| LinkingTo: |
Rcpp, RcppArmadillo, RcppThread |
| Suggests: |
knitr, missMDA, RhpcBLASctl, rmarkdown, testthat (≥ 3.0.0), withr |
| Published: |
2026-06-16 |
| DOI: |
10.32614/CRAN.package.slideimp |
| Author: |
Hung Pham  [aut,
cre, cph],
Posit Software, PBC [cph] (Copyright holder of code adapted from the
'carrier' package, MIT licensed) |
| Maintainer: |
Hung Pham <amser.hoanghung at gmail.com> |
| BugReports: |
https://github.com/hhp94/slideimp/issues |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: |
https://github.com/hhp94/slideimp,
https://hhp94.github.io/slideimp/ |
| NeedsCompilation: |
yes |
| Language: |
en-US |
| Citation: |
slideimp citation info |
| Materials: |
README, NEWS |
| CRAN checks: |
slideimp results |
Documentation:
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