extract_snps: Extract SNPs

In MRCIEU/mrQC: CheckSumStats

Extract SNPs

Description

Exract the summary data for the rsids of interest from a target study. This only works on linux/ mac operating systems. Will not work on Windows.

Usage

extract_snps(
  snplist = NULL,
  path_to_target_file = NULL,
  exact_match = TRUE,
  path_to_target_file_sep = "\t",
  Test.gz = FALSE,
  fill = FALSE,
  Comment = "#",
  Head = TRUE,
  get_sig_snps = FALSE,
  p_val_col_number = NULL,
  p_threshold = 5e-08
)

Arguments

snplist	a list of rsids of interest, either a character vector or path_to_target_file with the list of rsids
path_to_target_file	path to the target file This contains the summary data for the trait of #' interest
exact_match	search for exact matches. Default TRUE
path_to_target_file_sep	column/field separator. Default assumes that data is tab separated
Test.gz	is the target data a gz file? Default set to FALSE
fill	argument from read.table. logical. If ‘TRUE’ then in case the rows have unequal length, blank fields are implicitly added. Default is FALSE
Comment	comment to pass to comment.char in read.table. default = "#"
Head	Does the file have a header ? Default set to TRUE
get_sig_snps	also extract the top hits from the target file, not just the SNPs specified in snplist. logic TRUE or FALSE. Default set to FALSE
p_val_col_number	the column number corresponding to the P values for the SNP-trait associations
p_threshold	Extract SNP-trait associtions with P values less than this value. Default set to 5e-8

Value

data frame

MRCIEU/mrQC documentation built on May 6, 2023, 1:40 p.m.