Package: pould 1.0.1

pould: Phased or Unphased Linkage Disequilibrium

Computes the D', Wn, and conditional asymmetric linkage disequilibrium (ALD) measures for pairs of genetic loci. Performs these linkage disequilibrium (LD) calculations on phased genotype data recorded using Genotype List (GL) String or columnar formats. Alternatively, generates expectation-maximization (EM) estimated haplotypes from phased data, or performs LD calculations on EM estimated haplotypes. Performs sign tests comparing LD values for phased and unphased datasets, and generates heat-maps for each LD measure. Described by Osoegawa et al. (2019a) <doi:10.1016/j.humimm.2019.01.010>, and Osoegawa et. al. (2019b) <doi:10.1016/j.humimm.2019.05.018>.

Authors:Steven Mack [aut, cre]

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pould.pdf |pould.html✨
pould/json (API)
NEWS

# Install 'pould' in R:
install.packages('pould', repos = c('https://sjmack.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • drb1.dqb1.demo - Example HLA Genotype Data for DRB1 and DQB1
  • hla.hap.demo - Example Six-Locus HLA Haplotype Data in GL String Format

On CRAN:

Conda:

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

2.70 score 1 stars 2 scripts 137 downloads 7 exports 104 dependencies

Last updated 4 years agofrom:a808c93ff5. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 22 2025
R-4.5-winNOTEMar 22 2025
R-4.5-macNOTEMar 22 2025
R-4.5-linuxNOTEMar 22 2025
R-4.4-winNOTEMar 22 2025
R-4.4-macNOTEMar 22 2025
R-4.4-linuxNOTEMar 22 2025

Exports:cALDextractLociLD.heat.mapLD.sign.testLDWrapparseGenotypestrimAlleles

Dependencies:arsenalaskpassbackportsbase64encBIGDAWGbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforeignFormulafsgapgap.datasetsgenericsggplot2gluegridExtragtablehaplo.statshighrHmischtmlTablehtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixModelsmemoisemgcvmimemultcompmunsellmvtnormnlmennetopensslpillarpkgconfigplotlyplyrpolsplinepromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRdpackreshape2rlangrmarkdownrmsrpartrstudioapisandwichsassscalesSparseMstringistringrsurvivalsysTH.datatibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunXMLyamlzoo

pould: Phased Or Unphased Linkage Disequilibrium

Steven J. Mack, PhD -- [email protected]

Rendered frompould.Rmdusingknitr::rmarkdownon Mar 22 2025.

Last update: 2020-10-16
Started: 2020-04-15