drb1.dqb1.demo

A data frame of phased two-field HLA-DRB1 and HLA-DQB1 genotypes for 419 European American control subjects included
in a study of Multiple Sclerosis.
Genotype data for each locus is shown in two columns; the alleles in columns 1 and 2 are phased with the alleles in columns 3 and 4, respectively.
These genotypes were extracted from the hla.hap.demo dataset.

data

Genotype

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>.

Steven Mack

pould

Phased or Unphased Linkage Disequilibrium

drb1.dqb1.demo function

A data frame with 419 rows and four columns<ul>
<li>DRB1: the first of two two-field HLA-DRB1 alleles</li>
<li>DRB1: the second of two two-field HLA-DRB1 alleles</li>
<li>DQB1: the first of two two-field HLA-DQB1 alleles</li>
<li>DQB1: the second of two two-field HLA-DRB1 alleles</li>
</ul>

drb1.dqb1.demo: Example HLA Genotype Data for DRB1 and DQB1

Description

Usage

Arguments

Format

References