ld.plink: Compute pairwise LD between markers with PLINK

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Compute pairwise LD between markers with PLINK

Usage

ld.plink(prefix, dprime = FALSE, index.snp = NULL, markers = NULL,
  chr = NULL, from = NULL, to = NULL, window = NULL, window.r2 = 0,
  flags = "", ...)

Arguments

prefix	a pointer to a PLINK fileset (of class plink)
dprime	logical; if TRUE, compute Lewontin D-prime instead of R2
index.snp	name of the marker used to anchor the calculation
markers	compute all pairwise LD values between markers in this list
chr	limit analysis to this chromosome
from	with chr, limit analysis to window starting at this position
to	with chr, limit analysis to window ending at this position
window	(ignored)
window.r2	keep calculating until pairwise LD falls below this threshold
flags	command-line flags passed directly to underlying PLINK call
...	ignored

Details

Linkage disequlibrium (LD) is estimated here via the squared genetic correlation (r^2) between loci. Since the size of the output scales with the square of the number of markers and can easily grow to gigabytes for a dataset with >10k markers, it is highly recommended to limit the calculation using the parameters above.

See the relevant PLINK documentation for details of the underlying calculations.

Value

a data.table of pairwise LD values, one marker pair per row

References

PLINK v1.9: https://www.cog-genomics.org/plink2

Purcell S et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81(3): 559-575. doi:10.1086/519795.

Lewontin RC (1960) The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49(1): 49-67.

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.