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

## Documentation for package ‘poolfstat’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.