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 188 downloads 7 exports 104 dependencies

Last updated 4 years agofrom:a808c93ff5. Checks:1 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 20 2025
R-4.5-winNOTEFeb 20 2025
R-4.5-macNOTEFeb 20 2025
R-4.5-linuxNOTEFeb 20 2025
R-4.4-winNOTEFeb 20 2025
R-4.4-macNOTEFeb 20 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 Feb 20 2025.

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