calculate_LD: Calculate LD R^2 between pairs of loci

In FellouMada/rSNPdata: R package for Analysis of P. falciparum whole genome SNPs data

Calculate LD R^2 between pairs of loci

Description

Calculate LD R^2 between pairs of loci

Usage

snpdata = calculate_LD(snpdata, min.r2=0.2, inter.chrom=FALSE, chroms=c("Pf3D7_04_v3","Pf3D7_05_v3"))

Arguments

snpdata	SNPdata object
min.r2	the minimum r2 value below which the LD value is not reported
inter.chrom	whether to calculate inter-chromosomal LD. FALSE by default
chroms	a vector of chromosome names for which LD should be calculated

Details

the output file from LD calculation could be large. In order to reduce the size of that file, it's recommended to specify the list of chromosomes for which LD should be calculated using the 'chroms' option

Value

SNPdata object with an extra field: LD

FellouMada/rSNPdata documentation built on June 12, 2022, 7:29 p.m.