ld: Linkage disequilibrium (LD) computation from phased data

Description Usage Arguments Author(s)

Description

Function to compute linkage disequilibrium (LD) from phased data. The LD is computed between a SNP of interest and all other SNPs within a specified window around it.

Usage

1
	ld(phase_file, snps_file, output_file, window = 500000, coefficient = "dprime", maf = 0.0, gzip = TRUE)

Arguments

phase_file

The name of the input file with phased genotypes in the VCF format.

snps_file

The name of the input file with the list of SNP identifiers (one per line). The SNP identifier can be an rsID, chromosomal position in base-pairs or any other identifier format that is present in phase_file. For every SNP in the list, the LD between it and all other SNPs within a specified window around it is computed.

output_file

The name of the output file. Output file includes five tab-separated columns. The first four columns are: FIRST_MARKER, FIRST_BP, SECOND_MARKER, SECOND_BP. The last column depends on the specified coefficient and can be D, DPRIME or R2, accordingly.

window

The number of base pairs to consider around every SNP of interest.

coefficient

The LD coefficient to be calculated between a pair of SNPs. The supported LD coefficients are "d" (D), "dprime" (D') or "r2" (r^2).

maf

Minor Allele Frequency (MAF) threshold: SNPs with MAF <= maf will not be considered. The threshold may vary from 0 (default) to 0.5.

gzip

TRUE if output file is in gzip format.

Author(s)

Daniel Taliun, Johann Gamper, Cristian Pattaro


LDExplorer documentation built on May 2, 2019, 5:54 p.m.

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