check_pos_se {MungeSumstats}R Documentation

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_pos_se(
  sumstats_dt,
  path,
  pos_se,
  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.

pos_se

Binary Should the standard Error (SE) column be checked to ensure it is greater than 0? Those that are, are removed (if present in sumstats file). Default TRUE.

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


[Package MungeSumstats version 1.2.4 Index]