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poolfstat (version 3.1.0)

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

Description

Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, 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' and 'SelEstim' format, see the Package vignette for details).

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Version

Install

install.packages('poolfstat')

Monthly Downloads

357

Version

3.1.0

License

GPL (>= 2)

Maintainer

Mathieu Gautier

Last Published

February 23rd, 2026

Functions in poolfstat (3.1.0)

compute_snpQ2onepair

compute_snpQ2onepair

compute_F4DfromF2samples

compute_F4DfromF2samples

compute_F3fromF2samples

compute_F3fromF2samples

compute_snpQ2rw

compute_snpQ2rw

compute_snpQ1onepop

compute_snpQ1onepop

compute_snpQ1rw

compute_snpQ1rw

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

countdata2genobaypass

Convert a countdata object into BayPass input files.

Merge two pooldata or countdata objects

extract_nonvscan_counts

extract_nonvscan_counts

extract_allele_names

extract_allele_names

find.tree.popset

Find sets of populations that may used as scaffold tree

extract_vscan_counts

extract_vscan_counts

find_indelneighbor_idx

find_indelneighbor_idx

fitted.graph-class

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

S4 class to represent fstats results obtained with computeFstats.

Estimate parameters of an admixture graph

generate.jackknife.blocks

Generate block coordinates for block-jackknife

generate.graph.params

Generate a graph parameter object to fit admixture graph to observed fstats

generateF3names

generateF3names

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

genotreemix2countdata

Convert allele count input files from the Treemix program into a coundata object

genoselestim2pooldata

Convert SelEstim read count input files into a pooldata object

generateF4names

generateF4names

is.fitted.graph

Check fitted.graph objects

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

Check fstats objects

Check pairwisefst objects

is.graph.params

Check graph.params objects

Check pooldata objects

pooldata2genoselestim

Convert a pooldata object into SelEstim input files.

make.example.files

Create example files

pooldata2genobaypass

Convert a pooldata object into BayPass input files.

pooldata2diyabc

Convert a pooldata object into DIYABC input files.

Check countdata objects

heatmap,pairwisefst-method

Show pairwisefst object

graph.params-class

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

popsync2pooldata

Convert Popoolation Sync files into a pooldata object

randomallele.pca

PCA of a pooldata or countdata object using a random allele approach

Create a (pseudo-)pooled sample from a set of samples (using random-allele sampling)

show,fitted.graph-method

Show fitted.graph object

show,countdata-method

Show countdata object

plot,fstats-method

plot fstats object

scan_allele_info

scan_allele_info

plot,graph.params-method

plot graph in graph.params object

rooted.njtree.builder

Construct and root an Neighbor-Joining tree of presumably nonadmixed leaves

plot,fitted.graph-method

plot pairwisefst object

Implement a graph builder heuristic by successively adding leaves to an initial graph

pairwisefst-class

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

Convert a VCF file into a pooldata object.

show,fstats-method

Show fstats object

plot,pairwisefst-method

plot pairwisefst object

Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervals

show,graph.params-method

Show graph.params object

Simulate read counts from count data and return a pooldata object

show,pairwisefst-method

Show pairwisefst object

S4 class to represent a Pool-Seq data set.

sliding.windows.fstat

Compute sliding window estimates of F-statistics or ratio of F-statistics over the genome

pooldata.subset

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

show,pooldata-method

Show pooldata object

compute_F3fromF2

compute_F3fromF2

Compute Fst from Pool-Seq data or Count data

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

Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and within and across population diversity

compute.pairwiseFST

Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)

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_F4fromF2samples

compute_F4fromF2samples

compute_QmatfromF2samples

compute_QmatfromF2samples

compute_snpHierFstAov

compute_snpHierFstAov

compute_blockDdenom

compute_blockDdenom

compute_F4fromF2

compute_F4fromF2

compute_snpFstAov

compute_snpFstAov