Package: pould 1.0.2

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_1.0.2.tar.gz
pould_1.0.2.zip(r-4.7)pould_1.0.2.zip(r-4.6)pould_1.0.2.zip(r-4.5)
pould_1.0.2.tgz(r-4.6-any)pould_1.0.2.tgz(r-4.5-any)
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pould_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pould/json (API)

# 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:

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

3.00 score 2 stars 5 scripts 449 downloads 7 exports 75 dependencies

Last updated from:db952b3f1c. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	157
source / vignettes	OK	222
linux-release-x86_64	OK	153
macos-release-arm64	OK	91
macos-oldrel-arm64	OK	94
windows-devel	OK	91
windows-release	OK	115
windows-oldrel	OK	88
wasm-release	OK	155

Exports:cALD extractLoci LD.heat.map LD.sign.test LDWrap parseGenotypes trimAlleles

Dependencies:arsenal askpass base64enc BIGDAWG bslib cachem cli cpp11 crosstalk curl data.table digest dplyr evaluate farver fastmap fontawesome fs gap gap.datasets generics ggplot2 glue gtable haplo.stats highr htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle magrittr MASS memoise mime openssl otel pillar pkgconfig plotly plyr promises purrr R6 rappdirs rbibutils RColorBrewer Rcpp Rdpack reshape2 rlang rmarkdown S7 sass scales stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML yaml

pould: Phased Or Unphased Linkage Disequilibrium

Rendered frompould.Rmdusingknitr::rmarkdown

Last update: 2026-05-01
Started: 2020-04-15

Help page	Topics
Calculation of the D', Wn, and conditional Asymmetric LD Measures	cALD
Example HLA Genotype Data for DRB1 and DQB1	drb1.dqb1.demo
Extract Locus Information from Supplied Haplotype Data	extractLoci
Example Six-Locus HLA Haplotype Data in GL String Format	hla.hap.demo
Generates heat-maps for four linkage disequilibrium (LD) values (D', Wn, WLoc1/Loc2 and WLoc2/Loc1) generated for all pairs of phased and unphased two-locus haplotypes by LDWrap().	LD.heat.map
Perform the sign test on paired LD values for phased and unphased haplotypes	LD.sign.test
Parser for CSV-formatted GL String Haplotype Data	LDWrap
Reformat columnnar genotype data to GL String format	parseGenotypes
Truncate allele names in haplotypes to the specified number of fields.	trimAlleles
Exporting Haplotype Vectors	writeVector

Package: pould 1.0.2

pould: Phased or Unphased Linkage Disequilibrium

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Help Manual

Usage by other packages (reverse dependencies)