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poolfstat (version 2.1.1)

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

Description

Functions for the computation of f- and D-statistics (estimation of 'Fst', Patterson's 'F2', 'F3', 'F3*', 'F4' and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in 'TreeMix', 'BayPass' or 'SelEstim' format).

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Version

Install

install.packages('poolfstat')

Monthly Downloads

371

Version

2.1.1

License

GPL (>= 2)

Maintainer

Mathieu Gautier

Last Published

May 2nd, 2022

Functions in poolfstat (2.1.1)

compute.fstats

Estimate the F-statistics (F2, F3, F3star, F4, Dstat)
compare.fitted.fstats

Compare fitted f2, f3 and f4 f-statistics of an admixture graph with estimated ones
fit.graph

Estimate parameters of an admixture graph
countdata.subset

Create a subset of a countdata object that contains count data as a function of pop or SNP indexes
add.leaf

Test all possible connection of a leaf to a graph with non-admixed and or admixed edges
compute.pairwiseFST

Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)
find.tree.popset

Find sets of populations that may used as scaffold tree
compute.f4ratio

Compute F4ratio (estimation of admixture rate) from an fstats object
countdata-class

S4 class to represent a Count data set.
computeFST

Compute FST from Pool-Seq data or Count data
fstats-class

S4 class to represent fstats results obtained with computeFstats.
fitted.graph-class

S4 class to represent a population tree or admixture graph and its underlying fitted parameter.
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
genobaypass2pooldata

Convert BayPass read count and haploid pool size input files into a pooldata object
genobaypass2countdata

Convert BayPass allele count input files into a coundata object
graph.params2qpGraphFiles

Generate files for the qpGraph software from a graph.params object
is.fitted.graph

Check fitted.graph objects
generate.jackknife.blocks

Generate block coordinates for block-jackknife
generate.graph.params

Generate a graph parameter object to fit admixture graph to observed fstats
is.graph.params

Check graph.params objects
is.fstats

Check fstats objects
pooldata.subset

Create a subset of the pooldata object that contains Pool-Seq data as a function of pool and/or SNP indexes
vcf2pooldata

Convert a VCF file into a pooldata object.
show,pooldata-method

Show pooldata object
pooldata-class

S4 class to represent a Pool-Seq data set.
graph.params2symbolic.fstats

Provide a symbolic representation of all the F-statistics and the model system of equations
is.pairwisefst

Check pairwisefst objects
graph.builder

Implement a graph builder heuristic by successively adding leaves to an initial graph
show,pairwisefst-method

Show pairwisefst object
show,graph.params-method

Show graph.params object
make.example.files

Create example files
is.pooldata

Check pooldata objects
plot,fstats-method

plot fstats object
show,fitted.graph-method

Show fitted.graph object
plot,graph.params-method

plot graph in graph.params object
graph.params-class

S4 class to represent a population tree or admixture graph and its underlying parameter.
pairwisefst-class

S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST
pooldata2genoselestim

Convert a pooldata object into SelEstim input files.
show,countdata-method

Show countdata object
pooldata2genobaypass

Convert a pooldata object into BayPass input files.
rooted.njtree.builder

Construct and root an Neighbor-Joining tree of presumably nonadmixed leaves
plot,fitted.graph-method

plot pairwisefst object
is.countdata

Check countdata objects
heatmap,pairwisefst-method

Show pairwisefst object
plot,pairwisefst-method

plot pairwisefst object
poolfstat

PoolFstat
popsync2pooldata

Convert Popoolation Sync files into a pooldata object
plot_fstats

Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervals
show,fstats-method

Show fstats object