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

Documentation for package ‘poolfstat’ version 2.2.0

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PoolFstat

-- A --

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

-- B --

-- 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_Ddenom	compute_Ddenom
compute_Ddenom_bjmeans	compute_Ddenom_bjmeans
compute_F2_bjmeans	compute_F2_bjmeans
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_Q_bjmeans	compute_Q_bjmeans
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

-- E --

-- 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 --

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 --

Show pairwisefst object

-- I --

-- M --

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.
poolfstat	PoolFstat
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 --

-- V --

Convert a VCF file into a pooldata object.

-- misc --