Package: poolfstat 3.1.0

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

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, see the Package vignette for details).

Authors:Mathieu Gautier [aut, cre]

poolfstat_3.1.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
poolfstat/json (API)

# Install 'poolfstat' in R:

install.packages('poolfstat', repos = c('https://mgautierinra.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

4.07 score 291 scripts 547 downloads 4 mentions 69 exports 74 dependencies

Last updated from:47d0fe5e1b. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	146
linux-devel-x86_64	OK	163
source / vignettes	OK	257
linux-release-arm64	OK	148
linux-release-x86_64	OK	167
macos-release-arm64	OK	296
macos-release-x86_64	OK	386
macos-oldrel-arm64	OK	224
macos-oldrel-x86_64	OK	441
windows-devel-arm64	OK	590
windows-devel-x86_64	OK	156
windows-release-arm64	OK	430
windows-release-x86_64	OK	160
windows-oldrel-x86_64	OK	168
wasm-release	OK	124

Exports:.block_sum .block_sum2 .compute_blockDdenom .compute_F3fromF2 .compute_F3fromF2samples .compute_F4DfromF2samples .compute_F4fromF2 .compute_F4fromF2samples .compute_H1 .compute_Q2 .compute_QmatfromF2samples .compute_snpFstAov .compute_snpHierFstAov .compute_snpQ1 .compute_snpQ1onepop .compute_snpQ1rw .compute_snpQ2 .compute_snpQ2onepair .compute_snpQ2rw .extract_allele_names .extract_nonvscan_counts .extract_vscan_counts .find_indelneighbor_idx .generateF3names .generateF4names .scan_allele_info .simureads_mono .simureads_poly add.leaf compare.fitted.fstats compute.f4ratio compute.fstats compute.pairwiseFST computeFST countdata.subset countdata2genobaypass data.merge find.tree.popset fit.graph generate.graph.params generate.jackknife.blocks genobaypass2countdata genobaypass2pooldata genoselestim2pooldata genotreemix2countdata graph.builder graph.params2qpGraphFiles graph.params2symbolic.fstats heatmap is.countdata is.fitted.graph is.fstats is.graph.params is.pairwisefst is.pooldata make.example.files plot plot_fstats pooldata.subset pooldata2diyabc pooldata2genobaypass pooldata2genoselestim poolify popsync2pooldata randomallele.pca rooted.njtree.builder sim.readcounts sliding.windows.fstat vcf2pooldata

Dependencies:ape base64enc bit bit64 bslib cachem cli clipr codetools cpp11 crayon data.table DiagrammeR digest doParallel dplyr evaluate farver fastmap fontawesome foreach fs generics glue highr hms htmltools htmlwidgets igraph iterators jquerylib jsonlite knitr labeling lattice lifecycle magrittr Matrix memoise mime nlme nnls pillar pkgconfig prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppProgress readr rlang rmarkdown rstudioapi Ryacas sass scales stringi stringr tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite visNetwork vroom withr xfun yaml

poolfstatvignette

Rendered fromvignette.Rnwusingutils::Sweave

Last update: 2021-05-27
Started: 2021-05-27

Help page	Topics
Test all possible connection of a leaf to a graph with non-admixed and or admixed edges	add.leaf
bjack_cov	bjack_cov
block_sum	.block_sum block_sum
block_sum2	.block_sum2 block_sum2
Compare fitted f2, f3 and f4 f-statistics of an admixture graph with estimated ones	compare.fitted.fstats
compute_blockDdenom	.compute_blockDdenom compute_blockDdenom
compute_F3fromF2	.compute_F3fromF2 compute_F3fromF2
compute_F3fromF2samples	.compute_F3fromF2samples compute_F3fromF2samples
compute_F4DfromF2samples	.compute_F4DfromF2samples compute_F4DfromF2samples
compute_F4fromF2	.compute_F4fromF2 compute_F4fromF2
compute_F4fromF2samples	.compute_F4fromF2samples compute_F4fromF2samples
compute_H1	.compute_H1 compute_H1
compute_Q2	.compute_Q2 compute_Q2
compute_QmatfromF2samples	.compute_QmatfromF2samples compute_QmatfromF2samples
compute_snpFstAov	.compute_snpFstAov compute_snpFstAov
compute_snpHierFstAov	.compute_snpHierFstAov compute_snpHierFstAov
compute_snpQ1	.compute_snpQ1 compute_snpQ1
compute_snpQ1onepop	.compute_snpQ1onepop compute_snpQ1onepop
compute_snpQ1rw	.compute_snpQ1rw compute_snpQ1rw
compute_snpQ2	.compute_snpQ2 compute_snpQ2
compute_snpQ2onepair	.compute_snpQ2onepair compute_snpQ2onepair
compute_snpQ2rw	.compute_snpQ2rw compute_snpQ2rw
Compute F4ratio (estimation of admixture rate) from an fstats object	compute.f4ratio
Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and within and across population diversity	compute.fstats
Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)	compute.pairwiseFST
Compute Fst from Pool-Seq data or Count data	computeFST
S4 class to represent a Count data set.	countdata countdata-class
Create a subset of a countdata object that contains count data as a function of pop or SNP indexes	countdata.subset
Convert a countdata object into BayPass input files.	countdata2genobaypass
Merge two pooldata or countdata objects	data.merge
extract_allele_names	.extract_allele_names extract_allele_names
extract_nonvscan_counts	.extract_nonvscan_counts extract_nonvscan_counts
extract_vscan_counts	.extract_vscan_counts extract_vscan_counts
find_indelneighbor_idx	.find_indelneighbor_idx find_indelneighbor_idx
Find sets of populations that may used as scaffold tree	find.tree.popset
Estimate parameters of an admixture graph	fit.graph
S4 class to represent a population tree or admixture graph and its underlying fitted parameter.	fitted.graph fitted.graph-class gen.fitted.graph
S4 class to represent fstats results obtained with computeFstats.	fstats fstats-class
Generate a graph parameter object to fit admixture graph to observed fstats	generate.graph.params
Generate block coordinates for block-jackknife	generate.jackknife.blocks
generateF3names	.generateF3names generateF3names
generateF4names	.generateF4names generateF4names
Convert BayPass allele count input files into a coundata object	genobaypass2countdata
Convert BayPass read count and haploid pool size input files into a pooldata object	genobaypass2pooldata
Convert SelEstim read count input files into a pooldata object	genoselestim2pooldata
Convert allele count input files from the Treemix program into a coundata object	genotreemix2countdata
Implement a graph builder heuristic by successively adding leaves to an initial graph	graph.builder
S4 class to represent a population tree or admixture graph and its underlying parameter.	graph.params graph.params-class
Generate files for the qpGraph software from a graph.params object	graph.params2qpGraphFiles
Provide a symbolic representation of all the F-statistics and the model system of equations	graph.params2symbolic.fstats
Show pairwisefst object	heatmap,pairwisefst-method
Check countdata objects	is.countdata
Check fitted.graph objects	is.fitted.graph
Check fstats objects	is.fstats
Check graph.params objects	is.graph.params
Check pairwisefst objects	is.pairwisefst
Check pooldata objects	is.pooldata
Create example files	make.example.files
S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST	pairwisefst pairwisefst-class
Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervals	plot_fstats
plot pairwisefst object	plot,fitted.graph-method
plot fstats object	plot,fstats-method
plot graph in graph.params object	plot,graph.params-method
plot pairwisefst object	plot,pairwisefst-method
S4 class to represent a Pool-Seq data set.	pooldata pooldata-class
Create a subset of the pooldata object that contains Pool-Seq data as a function of pool and/or SNP indexes	pooldata.subset
Convert a pooldata object into DIYABC input files.	pooldata2diyabc
Convert a pooldata object into BayPass input files.	pooldata2genobaypass
Convert a pooldata object into SelEstim input files.	pooldata2genoselestim
Create a (pseudo-)pooled sample from a set of samples (using random-allele sampling)	poolify
poppair_idx	poppair_idx
Convert Popoolation Sync files into a pooldata object	popsync2pooldata
PCA of a pooldata or countdata object using a random allele approach	randomallele.pca
Construct and root an Neighbor-Joining tree of presumably nonadmixed leaves	rooted.njtree.builder
scan_allele_info	.scan_allele_info scan_allele_info
Show countdata object	show,countdata-method
Show fitted.graph object	show,fitted.graph-method
Show fstats object	show,fstats-method
Show graph.params object	show,graph.params-method
Show pairwisefst object	show,pairwisefst-method
Show pooldata object	show,pooldata-method
Simulate read counts from count data and return a pooldata object	sim.readcounts
simureads_mono	.simureads_mono simureads_mono
simureads_poly	.simureads_poly simureads_poly
Compute sliding window estimates of F-statistics or ratio of F-statistics over the genome	sliding.windows.fstat
Convert a VCF file into a pooldata object.	vcf2pooldata

Package: poolfstat 3.1.0

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

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