hla.hap.demo

A data frame of experimentally phased genotype data for the HLA-A, -C, -B, -DRB1, -DQB1 and DQB1 loci. These haplotypes are
for 419 unrelated European American control subjects included in a study of Multiple Sclerosis. These haplotypes were experimentally phased using the EM algorithm; low-frequency haplotypes (with counts &lt; 3) are assigned stochasically by the EM method, so the phase "quality" of these haplotypes should be considered lower than that for haplotypes determined via family segregation analysis.

data

haplotype

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

hla.hap.demo function

A data frame with 419 rows and two columns<ul>
<li>Relation: the genotyped individual's status in a family</li>
<li>Gl String: GL String formatted multilocus phased HLA genotype</li>
</ul>

hla.hap.demo: Example Six-Locus HLA Haplotype Data in GL String Format

Description

Usage

Arguments

Format

References