Package: fst4pg 1.0.0
fst4pg: Genetic Distance Segmentation for Population Genetics
Provides efficient methods to compute local and genome wide genetic distances (corresponding to the so called Hudson Fst parameters) through moment method, perform chromosome segmentation into homogeneous Fst genomic regions, and selection sweep detection for multi-population comparison. When multiple profile segmentation is required, the procedure can be parallelized using the future package.
Authors:
fst4pg_1.0.0.tar.gz
fst4pg_1.0.0.zip(r-4.5)fst4pg_1.0.0.zip(r-4.4)fst4pg_1.0.0.zip(r-4.3)
fst4pg_1.0.0.tgz(r-4.4-any)fst4pg_1.0.0.tgz(r-4.3-any)
fst4pg_1.0.0.tar.gz(r-4.5-noble)fst4pg_1.0.0.tar.gz(r-4.4-noble)
fst4pg_1.0.0.tgz(r-4.4-emscripten)fst4pg_1.0.0.tgz(r-4.3-emscripten)
fst4pg.pdf |fst4pg.html✨
fst4pg/json (API)
| # Install 'fst4pg' in R: |
| install.packages('fst4pg', repos = c('https://tmaryhuard.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:0f43b332a8. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 15 2024 |
| R-4.5-win | OK | Nov 15 2024 |
| R-4.5-linux | OK | Nov 15 2024 |
| R-4.4-win | OK | Nov 15 2024 |
| R-4.4-mac | OK | Nov 15 2024 |
| R-4.3-win | OK | Nov 15 2024 |
| R-4.3-mac | OK | Nov 15 2024 |
Exports:BuildFreqNbGContrastGraphSummaryContrastSummaryContrastTopRegionsFreq.filtHeatMapHudsonFst.gwHudsonFst.mHudsonFst.plotHudsonFst.profMakeProfile.opMakeProfile.sn_nomemoryProfilingSummaryRawPlot
Dependencies:bitopscaToolsclicodetoolscolorspacecpp11digestdplyrfansifarverfpopwfurrrfuturegenericsggplot2globalsgluegplotsgtablegtoolsisobandKernSmoothlabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert the Freq and NbGamete tables into a list. | BuildFreqNbG |
| Computation of the numerator of the moment estimator | Compute_Denominator |
| Computation of the numerator of the moment estimator | Compute_Nominator |
| ContrastGraphSummary | ContrastGraphSummary |
| ContrastSummary | ContrastSummary |
| ContrastTopRegions | ContrastTopRegions |
| DF4Plot1Prof | DF4Plot1Prof |
| Frequencies of the American and European HGDP populations | Freq |
| Filtering markers based on allelic frequencies | Freq.filt |
| HeatMap | HeatMap |
| HudsonFst.gw | HudsonFst.gw |
| HudsonFst.m | HudsonFst.m |
| Plot Fst values along chromosomes | HudsonFst.plot |
| HudsonFst.prof | HudsonFst.prof |
| Marker information | Info |
| MakeProfile.op | MakeProfile.op |
| MakeProfile.sn_nomemory | MakeProfile.sn_nomemory |
| MergeRegion | MergeRegion |
| Number of gametes of the American and European HGDP populations | NbGamete |
| Plot1Prof | Plot1Prof |
| ProfilingSummary | ProfilingSummary |
| Computation of the Fst moment estimator | Ratio_Average |
| RawPlot | RawPlot |
| Summarise1Profile | Summarise1Profile |
