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).
| Version: |
2.2.0 |
| Depends: |
R (≥ 3.0) |
| Imports: |
Rcpp (≥ 1.0.5), methods, data.table, utils, foreach, doParallel, parallel, DiagrammeR, ape, stats, zoo, Ryacas, Matrix, RcppProgress, progress, nnls |
| LinkingTo: |
Rcpp, RcppProgress |
| Published: |
2023-09-06 |
| DOI: |
10.32614/CRAN.package.poolfstat |
| Author: |
Mathieu Gautier |
| Maintainer: |
Mathieu Gautier <mathieu.gautier at inrae.fr> |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: |
yes |
| Citation: |
poolfstat citation info |
| Materials: |
ChangeLog |
| CRAN checks: |
poolfstat results |
Documentation:
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