LDprune: LD prune a genotype matrix

In bhattacharya-a-bt/MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies

LD prune a genotype matrix

Description

The function prunes SNPs that are in LD using PLINK

Usage

LDprune(
  W,
  snpList,
  snpLocs,
  fileName,
  windowSize,
  numSNPShift,
  ldThresh,
  verbose = T,
  snpAnnot = NULL
)

Arguments

W	matrix, dosage of SNPs
snpList	character vector, vector of SNPs in W
snpLocs	data frame, SNP locations in MatrixEQTL form
fileName	character, name for PLINK intermediate files
windowSize	integer, window size for PLINK pruning
numSNPShift	integer, shifting window for PLINK pruning
ldThresh	numeric, LD threshold for PLINK pruning

Value

list of pruned genotype matrix, vector of SNP names, and location data frame

bhattacharya-a-bt/MOSTWAS documentation built on April 6, 2023, 12:20 a.m.