Package: poolfstat 2.2.0

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

Functions for the computation of f- 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).

Authors:Mathieu Gautier

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poolfstat.pdf |poolfstat.html✨
poolfstat/json (API)

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

Peer review:

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.

56 exports 1.24 score 78 dependencies 4 mentions 110 scripts 403 downloads

Last updated 1 years agofrom:d81bab8c63. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-win-x86_64NOTESep 13 2024
R-4.5-linux-x86_64NOTESep 13 2024
R-4.4-win-x86_64NOTESep 13 2024
R-4.4-mac-x86_64NOTESep 13 2024
R-4.4-mac-aarch64NOTESep 13 2024
R-4.3-win-x86_64OKSep 13 2024
R-4.3-mac-x86_64OKSep 13 2024
R-4.3-mac-aarch64OKSep 13 2024

Exports:.compute_blockDdenom.compute_Ddenom.compute_Ddenom_bjmeans.compute_F2_bjmeans.compute_F3fromF2.compute_F3fromF2samples.compute_F4DfromF2samples.compute_F4fromF2.compute_F4fromF2samples.compute_H1.compute_Q_bjmeans.compute_Q2.compute_QmatfromF2samples.extract_allele_names.extract_nonvscan_counts.extract_vscan_counts.find_indelneighbor_idx.generateF3names.generateF4names.scan_allele_infoadd.leafcompare.fitted.fstatscompute.f4ratiocompute.fstatscompute.pairwiseFSTcomputeFSTcountdata.subsetfind.tree.popsetfit.graphgenerate.graph.paramsgenerate.jackknife.blocksgenobaypass2countdatagenobaypass2pooldatagenoselestim2pooldatagenotreemix2countdatagraph.buildergraph.params2qpGraphFilesgraph.params2symbolic.fstatsheatmapis.countdatais.fitted.graphis.fstatsis.graph.paramsis.pairwisefstis.pooldatamake.example.filesplotplot_fstatspooldata.subsetpooldata2diyabcpooldata2genobaypasspooldata2genoselestimpopsync2pooldatarandomallele.pcarooted.njtree.buildervcf2pooldata

Dependencies:apebase64encbitbit64bslibcachemclicliprcodetoolscolorspacecpp11crayondata.tableDiagrammeRdigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachfsgenericsgluehighrhmshtmltoolshtmlwidgetsigraphiteratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMatrixmemoisemimemunsellnlmennlspillarpkgconfigprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppProgressreadrrlangrmarkdownrstudioapiRyacassassscalesstringistringrtibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunyamlzoo

poolfstatvignette

Rendered fromvignette.Rnwusingutils::Sweaveon Sep 13 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Test all possible connection of a leaf to a graph with non-admixed and or admixed edgesadd.leaf
bjack_covbjack_cov
Compare fitted f2, f3 and f4 f-statistics of an admixture graph with estimated onescompare.fitted.fstats
compute_blockDdenom.compute_blockDdenom compute_blockDdenom
compute_Ddenom.compute_Ddenom compute_Ddenom
compute_Ddenom_bjmeans.compute_Ddenom_bjmeans compute_Ddenom_bjmeans
compute_F2_bjmeans.compute_F2_bjmeans compute_F2_bjmeans
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_Q_bjmeans.compute_Q_bjmeans compute_Q_bjmeans
compute_Q2.compute_Q2 compute_Q2
compute_QmatfromF2samples.compute_QmatfromF2samples compute_QmatfromF2samples
Compute F4ratio (estimation of admixture rate) from an fstats objectcompute.f4ratio
Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and within and across population diversitycompute.fstats
Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)compute.pairwiseFST
Compute FST from Pool-Seq data or Count datacomputeFST
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 indexescountdata.subset
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 treefind.tree.popset
Estimate parameters of an admixture graphfit.graph
S4 class to represent a population tree or admixture graph and its underlying fitted parameter.fitted.graph fitted.graph-class
S4 class to represent fstats results obtained with computeFstats.fstats fstats-class
Generate a graph parameter object to fit admixture graph to observed fstatsgenerate.graph.params
Generate block coordinates for block-jackknifegenerate.jackknife.blocks
generateF3names.generateF3names generateF3names
generateF4names.generateF4names generateF4names
Convert BayPass allele count input files into a coundata objectgenobaypass2countdata
Convert BayPass read count and haploid pool size input files into a pooldata objectgenobaypass2pooldata
Convert SelEstim read count input files into a pooldata objectgenoselestim2pooldata
Convert allele count input files from the Treemix program into a coundata objectgenotreemix2countdata
Implement a graph builder heuristic by successively adding leaves to an initial graphgraph.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 objectgraph.params2qpGraphFiles
Provide a symbolic representation of all the F-statistics and the model system of equationsgraph.params2symbolic.fstats
Show pairwisefst objectheatmap,pairwisefst-method
Check countdata objectsis.countdata
Check fitted.graph objectsis.fitted.graph
Check fstats objectsis.fstats
Check graph.params objectsis.graph.params
Check pairwisefst objectsis.pairwisefst
Check pooldata objectsis.pooldata
Create example filesmake.example.files
S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFSTpairwisefst pairwisefst-class
Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervalsplot_fstats
plot pairwisefst objectplot,fitted.graph-method
plot fstats objectplot,fstats-method
plot graph in graph.params objectplot,graph.params-method
plot pairwisefst objectplot,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 indexespooldata.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
PoolFstatpoolfstat-package poolfstat
poppair_idxpoppair_idx
Convert Popoolation Sync files into a pooldata objectpopsync2pooldata
PCA of a pooldata or countdata object using a random allele approachrandomallele.pca
Construct and root an Neighbor-Joining tree of presumably nonadmixed leavesrooted.njtree.builder
scan_allele_info.scan_allele_info scan_allele_info
Show countdata objectshow,countdata-method
Show fitted.graph objectshow,fitted.graph-method
Show fstats objectshow,fstats-method
Show graph.params objectshow,graph.params-method
Show pairwisefst objectshow,pairwisefst-method
Show pooldata objectshow,pooldata-method
Convert a VCF file into a pooldata object.vcf2pooldata