check_chr: Standardize the CHR column

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Standardize the CHR column

Description

Maps chromosome names to the default Ensembl/NCBI naming style and removes SNPs with nonstandard CHR entries. Optionally, also removes SNPs on user-specified chromosomes.

Usage

check_chr(
  sumstats_dt,
  log_files,
  check_save_out,
  rmv_chr,
  nThread,
  tabix_index,
  log_folder_ind
)

Arguments

sumstats_dt	data.table with summary statistics
log_files	list of locations for all log files
check_save_out	list of parameters for saved files
rmv_chr	Chromosomes to exclude from the formatted summary statistics file. Use NULL if no filtering is necessary. Default is c("X", "Y", "MT") which removes all non-autosomal SNPs.
nThread	Number of threads to use for parallel processes.
tabix_index	Index the formatted summary statistics with tabix for fast querying.
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.

Value

list containing the updated summary statistics data.table and the updated log file locations list

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.