check_dup_bp: Ensure all rows have unique positions, drop those that don't

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Ensure all rows have unique positions, drop those that don't

Description

Ensure all rows have unique positions, drop those that don't

Usage

check_dup_bp(
  sumstats_dt,
  bi_allelic_filter,
  check_dups,
  indels,
  path,
  log_folder_ind,
  check_save_out,
  tabix_index,
  nThread,
  log_files
)

Arguments

bi_allelic_filter	Binary Should non-biallelic SNPs be removed. Default is TRUE.
check_dups	whether to check for duplicates - if formatting QTL datasets this should be set to FALSE otherwise keep as TRUE. Default is TRUE.
indels	Binary does your Sumstats file contain Indels? These don't exist in our reference file so they will be excluded from checks if this value is TRUE. Default is TRUE.
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.
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 log files list

neurogenomics/MungeSumstats documentation built on May 2, 2024, 9:04 a.m.