check_signed_col: Ensure that there is at least one signed column in summary...

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Ensure that there is at least one signed column in summary statistics file Impute beta if user requests

Description

Ensure that there is at least one signed column in summary statistics file Impute beta if user requests

Usage

check_signed_col(
  sumstats_dt,
  impute_beta,
  log_folder_ind,
  rsids,
  imputation_ind,
  check_save_out,
  tabix_index,
  log_files,
  nThread
)

Arguments

sumstats_dt	data table obj of the summary statistics file for the GWAS
impute_beta	Binary, whether BETA should be imputed using other effect data if it isn't present in the sumstats. Note that this imputation is an approximation (for Z & SE approach) so could have an effect on downstream analysis. Use with caution. The different methods MungeSumstats will try and impute beta (in this order or priority) are: log(OR) 2. Z x SE Default value 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.
imputation_ind	Binary Should a column be added for each imputation step to show what SNPs have imputed values for differing fields. This includes a field denoting SNP allele flipping (flipped). On the flipped value, this denoted whether the alelles where switched based on MungeSumstats initial choice of A1, A2 from the input column headers and thus may not align with what the creator intended.Note these columns will be in the formatted summary statistics returned. Default is FALSE.
tabix_index	Index the formatted summary statistics with tabix for fast querying.
log_files	list of log file locations
nThread	Number of threads to use for parallel processes.

Value

null

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