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

## Documentation for package ‘poolfstat’ version 3.0.0

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

## Help Pages

A B C E F G H I M P R S V misc

## -- A --

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

## -- B --

bjack_cov | bjack_cov
block_sum | block_sum
block_sum2 | block_sum2

## -- C --

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) and within and across population diversity
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
compute_blockDdenom | compute_blockDdenom
compute_F3fromF2 | compute_F3fromF2
compute_F3fromF2samples | compute_F3fromF2samples
compute_F4DfromF2samples | compute_F4DfromF2samples
compute_F4fromF2 | compute_F4fromF2
compute_F4fromF2samples | compute_F4fromF2samples
compute_H1 | compute_H1
compute_Q2 | compute_Q2
compute_QmatfromF2samples | compute_QmatfromF2samples
compute_snpFstAov | compute_snpFstAov
compute_snpHierFstAov | compute_snpHierFstAov
compute_snpQ1 | compute_snpQ1
compute_snpQ1onepop | compute_snpQ1onepop
compute_snpQ1rw | compute_snpQ1rw
compute_snpQ2 | compute_snpQ2
compute_snpQ2onepair | compute_snpQ2onepair
compute_snpQ2rw | compute_snpQ2rw
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
countdata2genobaypass | Convert a countdata object into BayPass input files.

## -- E --

extract_allele_names | extract_allele_names
extract_nonvscan_counts | extract_nonvscan_counts
extract_vscan_counts | extract_vscan_counts

## -- F --

find.tree.popset | Find sets of populations that may used as scaffold tree
find_indelneighbor_idx | find_indelneighbor_idx
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.

## -- G --

gen.fitted.graph | S4 class to represent a population tree or admixture graph and its underlying fitted parameter.
generate.graph.params | Generate a graph parameter object to fit admixture graph to observed fstats
generate.jackknife.blocks | Generate block coordinates for block-jackknife
generateF3names | generateF3names
generateF4names | generateF4names
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

## -- H --

heatmap-method | Show pairwisefst object

## -- I --

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

## -- M --

make.example.files | Create example files

## -- P --

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
pooldata2diyabc | Convert a pooldata object into DIYABC input files.
pooldata2genobaypass | Convert a pooldata object into BayPass input files.
pooldata2genoselestim | Convert a pooldata object into SelEstim input files.
poppair_idx | poppair_idx
popsync2pooldata | Convert Popoolation Sync files into a pooldata object

## -- R --

randomallele.pca | PCA of a pooldata or countdata object using a random allele approach
rooted.njtree.builder | Construct and root an Neighbor-Joining tree of presumably nonadmixed leaves

## -- S --

scan_allele_info | scan_allele_info
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
sim.readcounts | Simulate read counts from count data and return a pooldata object
simureads_mono | simureads_mono
simureads_poly | simureads_poly
sliding.windows.fstat | Compute sliding window estimates of F-statistics or ratio of F-statistics over the genome

## -- V --

vcf2pooldata | Convert a VCF file into a pooldata object.

## -- misc --

.block_sum | block_sum
.block_sum2 | block_sum2
.compute_blockDdenom | compute_blockDdenom
.compute_F3fromF2 | compute_F3fromF2
.compute_F3fromF2samples | compute_F3fromF2samples
.compute_F4DfromF2samples | compute_F4DfromF2samples
.compute_F4fromF2 | compute_F4fromF2
.compute_F4fromF2samples | compute_F4fromF2samples
.compute_H1 | compute_H1
.compute_Q2 | compute_Q2
.compute_QmatfromF2samples | compute_QmatfromF2samples
.compute_snpFstAov | compute_snpFstAov
.compute_snpHierFstAov | compute_snpHierFstAov
.compute_snpQ1 | compute_snpQ1
.compute_snpQ1onepop | compute_snpQ1onepop
.compute_snpQ1rw | compute_snpQ1rw
.compute_snpQ2 | compute_snpQ2
.compute_snpQ2onepair | compute_snpQ2onepair
.compute_snpQ2rw | compute_snpQ2rw
.extract_allele_names | extract_allele_names
.extract_nonvscan_counts | extract_nonvscan_counts
.extract_vscan_counts | extract_vscan_counts
.find_indelneighbor_idx | find_indelneighbor_idx
.generateF3names | generateF3names
.generateF4names | generateF4names
.scan_allele_info | scan_allele_info
.simureads_mono | simureads_mono
.simureads_poly | simureads_poly