Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data


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Documentation for package ‘poolfstat’ version 2.0.0

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add.leaf Test all possible connection of a leaf to a graph with non-admixed and or admixed edges
compare.fitted.fstats Compare fitted f2, f3 and f4 f-statistics of an admixture graph with estimated ones
compute.f4ratio Compute F4ratio (estimation of admixture rate) from an fstats object
compute.fstats Estimate the F-statistics (F2, F3, F3star, F4, Dstat)
compute.pairwiseFST Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)
computeFST Compute FST from Pool-Seq data or Count data
countdata S4 class to represent a Count data set.
countdata-class S4 class to represent a Count data set.
countdata.subset Create a subset of a countdata object that contains count data as a function of pop or SNP indexes
find.tree.popset Find sets of populations that may used as scaffold tree
fit.graph Estimate parameters of an admixture graph
fitted.graph S4 class to represent a population tree or admixture graph and its underlying fitted parameter.
fitted.graph-class S4 class to represent a population tree or admixture graph and its underlying fitted parameter.
fstats S4 class to represent fstats results obtained with computeFstats.
fstats-class S4 class to represent fstats results obtained with computeFstats.
generate.graph.params Generate a graph parameter object to fit admixture graph to observed fstats
generate.jackknife.blocks Generate block coordinates for block-jackknife
genobaypass2countdata Convert BayPass allele count input files into a coundata object
genobaypass2pooldata Convert BayPass read count and haploid pool size input files into a pooldata object
genoselestim2pooldata Convert SelEstim read count input files into a pooldata object
genotreemix2countdata Convert allele count input files from the Treemix program into a coundata object
graph.builder Implement a graph builder heuristic by successively adding leaves to an initial graph
graph.params S4 class to represent a population tree or admixture graph and its underlying parameter.
graph.params-class S4 class to represent a population tree or admixture graph and its underlying parameter.
graph.params2qpGraphFiles Generate files for the qpGraph software from a graph.params object
graph.params2symbolic.fstats Provide a symbolic representation of all the F-statistics and the model system of equations
heatmap-method Show pairwisefst object
is.countdata Check countdata objects
is.fitted.graph Check fitted.graph objects
is.fstats Check fstats objects
is.graph.params Check graph.params objects
is.pairwisefst Check pairwisefst objects
is.pooldata Check pooldata objects
make.example.files Create example files
pairwisefst S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST
pairwisefst-class S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST
plot-method plot pairwisefst object
plot-method plot fstats object
plot-method plot graph in graph.params object
plot-method plot pairwisefst object
plot_fstats Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervals
pooldata S4 class to represent a Pool-Seq data set.
pooldata-class S4 class to represent a Pool-Seq data set.
pooldata.subset Create a subset of the pooldata object that contains Pool-Seq data as a function of pool and/or SNP indexes
pooldata2genobaypass Convert a pooldata object into BayPass input files.
pooldata2genoselestim Convert a pooldata object into SelEstim input files.
poolfstat PoolFstat
popsync2pooldata Convert Popoolation Sync files into a pooldata object
rooted.njtree.builder Construct and root an Neighbor-Joining tree of presumably nonadmixed leaves
show-method Show countdata object
show-method Show fitted.graph object
show-method Show fstats object
show-method Show graph.params object
show-method Show pairwisefst object
show-method Show pooldata object
vcf2pooldata Convert a VCF file into a pooldata object.