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. |