check_effect_columns_nonzero: Ensure that the standard error (se) is positive for all SNPs

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Ensure that the standard error (se) is positive for all SNPs

Description

Ensure that the standard error (se) is positive for all SNPs

Usage

check_effect_columns_nonzero(
  sumstats_dt,
  path,
  effect_columns_nonzero,
  log_folder_ind,
  check_save_out,
  tabix_index,
  nThread,
  log_files
)

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.
effect_columns_nonzero	Binary should the effect columns in the data BETA,OR (odds ratio),LOG_ODDS,SIGNED_SUMSTAT be checked to ensure no SNP=0. Those that do are removed(if present in sumstats file). Default FALSE.
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

Value

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

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