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]

pould_1.0.1.tar.gz
pould_1.0.1.zip(r-4.5)pould_1.0.1.zip(r-4.4)
pould_1.0.1.tgz(r-4.4-any)
pould_1.0.1.tar.gz(r-4.5-noble)pould_1.0.1.tar.gz(r-4.4-noble)
pould_1.0.1.tgz(r-4.4-emscripten)
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'))

Peer review:

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:

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 137 downloads 7 exports 104 dependencies

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

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winNOTENov 22 2024
R-4.5-linuxNOTENov 22 2024
R-4.4-winNOTENov 22 2024
R-4.4-macNOTENov 22 2024

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 Nov 22 2024.

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