LD prune a genotype matrix

The function prunes SNPs that are in LD using PLINK

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