check_info_score {MungeSumstats}R Documentation

Ensure all SNPs have info score above threshold

Description

Ensure all SNPs have info score above threshold

Usage

check_info_score(
  sumstats_dt,
  path,
  INFO_filter,
  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.

INFO_filter

numeric The minimum value permissible of the imputation information score (if present in sumstats file). Default 0.9.

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 1.2.1 Index]