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poolfstat (version 3.0.0)

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

Description

Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, 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 and SelEstim format).

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Version

Install

install.packages('poolfstat')

Monthly Downloads

317

Version

3.0.0

License

GPL (>= 2)

Maintainer

Mathieu Gautier

Last Published

November 23rd, 2024

Functions in poolfstat (3.0.0)

compute_blockDdenom

compute_blockDdenom
compute_F4DfromF2samples

compute_F4DfromF2samples
compute_snpQ2onepair

compute_snpQ2onepair
compute_snpQ2rw

compute_snpQ2rw
compute_snpQ2

compute_snpQ2
compute_snpQ1rw

compute_snpQ1rw
countdata2genobaypass

Convert a countdata object into BayPass input files.
compute_snpQ1onepop

compute_snpQ1onepop
extract_allele_names

extract_allele_names
compute_snpQ1

compute_snpQ1
fstats-class

S4 class to represent fstats results obtained with computeFstats.
generate.jackknife.blocks

Generate block coordinates for block-jackknife
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.
generate.graph.params

Generate a graph parameter object to fit admixture graph to observed fstats
generateF3names

generateF3names
extract_vscan_counts

extract_vscan_counts
graph.params2qpGraphFiles

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

extract_nonvscan_counts
graph.params-class

S4 class to represent a population tree or admixture graph and its underlying parameter.
graph.params2symbolic.fstats

Provide a symbolic representation of all the F-statistics and the model system of equations
heatmap,pairwisefst-method

Show pairwisefst object
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
is.fstats

Check fstats objects
find.tree.popset

Find sets of populations that may used as scaffold tree
is.countdata

Check countdata objects
is.fitted.graph

Check fitted.graph objects
is.pooldata

Check pooldata objects
pooldata2genobaypass

Convert a pooldata object into BayPass input files.
is.graph.params

Check graph.params objects
is.pairwisefst

Check pairwisefst objects
plot,fitted.graph-method

plot pairwisefst object
plot,pairwisefst-method

plot pairwisefst object
find_indelneighbor_idx

find_indelneighbor_idx
pooldata2genoselestim

Convert a pooldata object into SelEstim input files.
show,pairwisefst-method

Show pairwisefst object
poppair_idx

poppair_idx
poolfstat

PoolFstat
show,fstats-method

Show fstats object
plot,graph.params-method

plot graph in graph.params object
show,pooldata-method

Show pooldata object
plot,fstats-method

plot fstats object
pooldata.subset

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

Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervals
pooldata-class

S4 class to represent a Pool-Seq data set.
vcf2pooldata

Convert a VCF file into a pooldata object.
popsync2pooldata

Convert Popoolation Sync files into a pooldata object
pooldata2diyabc

Convert a pooldata object into DIYABC input files.
fit.graph

Estimate parameters of an admixture graph
rooted.njtree.builder

Construct and root an Neighbor-Joining tree of presumably nonadmixed leaves
randomallele.pca

PCA of a pooldata or countdata object using a random allele approach
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
make.example.files

Create example files
fitted.graph-class

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

Show graph.params object
scan_allele_info

scan_allele_info
pairwisefst-class

S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST
show,fitted.graph-method

Show fitted.graph object
sim.readcounts

Simulate read counts from count data and return a pooldata object
show,countdata-method

Show countdata object
sliding.windows.fstat

Compute sliding window estimates of F-statistics or ratio of F-statistics over the genome
simureads_poly

simureads_poly
simureads_mono

simureads_mono
block_sum

block_sum
block_sum2

block_sum2
add.leaf

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

bjack_cov
compare.fitted.fstats

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

Compute Fst from Pool-Seq data or Count data
compute.f4ratio

Compute F4ratio (estimation of admixture rate) from an fstats object
compute_F3fromF2

compute_F3fromF2
compute_snpFstAov

compute_snpFstAov
compute_H1

compute_H1
compute_F4fromF2

compute_F4fromF2
compute.fstats

Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and within and across population diversity
compute_Q2

compute_Q2
compute_snpHierFstAov

compute_snpHierFstAov
compute_F3fromF2samples

compute_F3fromF2samples
compute.pairwiseFST

Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)
compute_F4fromF2samples

compute_F4fromF2samples
compute_QmatfromF2samples

compute_QmatfromF2samples