LD prune a genotype matrix

The function prunes SNPs that are in LD using PLINK

eQTL_MOSTWAS(
  SNP_file_name,
  snps_location_file_name,
  SNP_file_name_dis = NULL,
  expression_file_name,
  gene_location_file_name,
  mediators_file_name,
  meds_location_file_name,
  covariates_file_name,
  output_file_name_loc_qtl,
  output_file_name_dis_qtl,
  output_file_name_loc_med = NULL,
  output_file_name_dis_med = NULL,
  p_loc_qtl = 1e-06,
  p_dis_qtl = 1e-06,
  FDRcut = 0.05,
  useModel = modelLINEAR,
  DePMA = F
)

Arguments

SNP_file_name	character, file name for SNP dosages in MatrixEQTL format
snps_location_file_name	character, file name for SNP locations in MatrixEQTL format
SNP_file_name_dis	character, file name for SNP distal dosages
expression_file_name	character, file name for gene expressions
gene_location_file_name	character, file name for gene locations
mediators_file_name	character, file name for mediator intensities
meds_location_file_name	character, file name for mediator locations as genes
output_file_name_loc_qtl	character, file name for first local QTLs
output_file_name_dis_qtl	character, file name for first distal QTLs
output_file_name_loc_med	character, file name for second local QTLs
output_file_name_dis_med	character, file name for second distal QTLs
p_loc_qtl	numeric, P-value threshold for first QTLs for DePMA
p_dis_qtl	numeric, P-value threshold for first QTLs for DePMA
FDRcut	numeric, FDR-adjusted P-value threshold for second QTLs for DePMA
useModel	MatrixEQTL model type
DePMA	logical, T/F if this analysis is for DePMA
covariates_files_name	character, file name for covariaties

Value

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