check_strand_ambiguous: Remove SNPs with strand-ambiguous alleles

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Remove SNPs with strand-ambiguous alleles

Description

Remove SNPs with strand-ambiguous alleles

Usage

check_strand_ambiguous(
  sumstats_dt,
  path,
  ref_genome,
  strand_ambig_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.
ref_genome	name of the reference genome used for the GWAS ("GRCh37" or "GRCh38"). Argument is case-insensitive. Default is NULL which infers the reference genome from the data.
strand_ambig_filter	Binary Should SNPs with strand-ambiguous alleles be removed. Default is 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.