check_chr {MungeSumstats}R Documentation

Ensure all SNPs on specified chromosomes are removed

Description

Ensure all SNPs on specified chromosomes are removed

Usage

check_chr(
  sumstats_dt,
  path,
  rmv_chr,
  log_folder_ind,
  check_save_out,
  tabix_index,
  nThread,
  log_files,
  make_uppercase = TRUE,
  rmv_chrPrefix = TRUE
)

Arguments

path

Filepath for the summary statistics file to be formatted. A dataframe or datatable of the summary statistics file can also be passed directly to MungeSumstats using the path parameter.

rmv_chr

vector or character The chromosomes on which the SNPs should be removed. Use NULL if no filtering necessary. Default is X, Y and mitochondrial.

log_folder_ind

Binary Should log files be stored containing all filtered out SNPs (separate file per filter). The data is outputted in the same format specified for the resulting sumstats file. The only exception to this rule is if output is vcf, then log file saved as .tsv.gz. Default is FALSE.

tabix_index

Index the formatted summary statistics with tabix for fast querying.

nThread

Number of threads to use for parallel processes.

log_files

list of log file locations

rmv_chrPrefix

Remove "chr" or "CHR" from chromosome names. Default is TRUE.

Value

list containing sumstats_dt, the modified summary statistics data table object and the log file list


[Package MungeSumstats version 1.2.0 Index]