check_drop_indels: Drop Indels from summary statistics

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Drop Indels from summary statistics

Description

Drop Indels from summary statistics

Usage

check_drop_indels(
  sumstats_dt,
  drop_indels,
  path,
  log_folder_ind,
  check_save_out,
  tabix_index,
  nThread,
  log_files
)

Arguments

sumstats_dt	data table obj of the summary statistics file for the GWAS
drop_indels	Binary, should any indels found in the sumstats be dropped? These can not be checked against a reference dataset and will have the same RS ID and position as SNPs which can affect downstream analysis. Default is False.
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.

Value

list containing sumstats_dt, the modified summary statistics data table object

Source

sumstats_dt <- MungeSumstats:::formatted_example() sumstats <- check_drop_indels(sumstats_dt = sumstats_dt, drop_indels = TRUE)

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