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poolfstat (version 2.2.0)

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

Description

Functions for the computation of f- and D-statistics (estimation of 'Fst', 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' or 'SelEstim' format).

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Version

Install

install.packages('poolfstat')

Monthly Downloads

317

Version

2.2.0

License

GPL (>= 2)

Maintainer

Mathieu Gautier

Last Published

September 6th, 2023

Functions in poolfstat (2.2.0)

compute_QmatfromF2samples

compute_QmatfromF2samples
extract_nonvscan_counts

extract_nonvscan_counts
add.leaf

Test all possible connection of a leaf to a graph with non-admixed and or admixed edges
compute_F4fromF2samples

compute_F4fromF2samples
generateF4names

generateF4names
pooldata-class

S4 class to represent a Pool-Seq data set.
generate.graph.params

Generate a graph parameter object to fit admixture graph to observed fstats
genoselestim2pooldata

Convert SelEstim read count input files into a pooldata object
find_indelneighbor_idx

find_indelneighbor_idx
compute_H1

compute_H1
bjack_cov

bjack_cov
scan_allele_info

scan_allele_info
heatmap,pairwisefst-method

Show pairwisefst object
plot,pairwisefst-method

plot pairwisefst object
show,pooldata-method

Show pooldata object
graph.params2symbolic.fstats

Provide a symbolic representation of all the F-statistics and the model system of equations
poolfstat

PoolFstat
computeFST

Compute FST from Pool-Seq data or Count data
compute.fstats

Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and within and across population diversity
plot,graph.params-method

plot graph in graph.params object
compute.f4ratio

Compute F4ratio (estimation of admixture rate) from an fstats object
compare.fitted.fstats

Compare fitted f2, f3 and f4 f-statistics of an admixture graph with estimated ones
show,fitted.graph-method

Show fitted.graph object
compute_F3fromF2

compute_F3fromF2
generateF3names

generateF3names
compute_Ddenom

compute_Ddenom
is.graph.params

Check graph.params objects
compute_F4DfromF2samples

compute_F4DfromF2samples
extract_allele_names

extract_allele_names
vcf2pooldata

Convert a VCF file into a pooldata object.
compute_F4fromF2

compute_F4fromF2
is.countdata

Check countdata objects
fstats-class

S4 class to represent fstats results obtained with computeFstats.
fitted.graph-class

S4 class to represent a population tree or admixture graph and its underlying fitted parameter.
genotreemix2countdata

Convert allele count input files from the Treemix program into a coundata object
compute_Q2

compute_Q2
show,fstats-method

Show fstats object
compute.pairwiseFST

Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)
find.tree.popset

Find sets of populations that may used as scaffold tree
compute_Q_bjmeans

compute_Q_bjmeans
pairwisefst-class

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

Check pairwisefst objects
graph.params2qpGraphFiles

Generate files for the qpGraph software from a graph.params object
compute_blockDdenom

compute_blockDdenom
fit.graph

Estimate parameters of an admixture graph
genobaypass2pooldata

Convert BayPass read count and haploid pool size input files into a pooldata object
poppair_idx

poppair_idx
pooldata.subset

Create a subset of the pooldata object that contains Pool-Seq data as a function of pool and/or SNP indexes
genobaypass2countdata

Convert BayPass allele count input files into a coundata object
pooldata2genoselestim

Convert a pooldata object into SelEstim input files.
is.fstats

Check fstats objects
extract_vscan_counts

extract_vscan_counts
is.fitted.graph

Check fitted.graph objects
generate.jackknife.blocks

Generate block coordinates for block-jackknife
plot,fstats-method

plot fstats object
plot_fstats

Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervals
plot,fitted.graph-method

plot pairwisefst object
popsync2pooldata

Convert Popoolation Sync files into a pooldata object
rooted.njtree.builder

Construct and root an Neighbor-Joining tree of presumably nonadmixed leaves
show,countdata-method

Show countdata object
compute_F3fromF2samples

compute_F3fromF2samples
compute_Ddenom_bjmeans

compute_Ddenom_bjmeans
countdata.subset

Create a subset of a countdata object that contains count data as a function of pop or SNP indexes
countdata-class

S4 class to represent a Count data set.
graph.builder

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

Check pooldata objects
compute_F2_bjmeans

compute_F2_bjmeans
pooldata2diyabc

Convert a pooldata object into DIYABC input files.
make.example.files

Create example files
randomallele.pca

PCA of a pooldata or countdata object using a random allele approach
pooldata2genobaypass

Convert a pooldata object into BayPass input files.
graph.params-class

S4 class to represent a population tree or admixture graph and its underlying parameter.
show,graph.params-method

Show graph.params object
show,pairwisefst-method

Show pairwisefst object