check_pos_se: Ensure that the standard error (se) is positive for all SNPs...

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Ensure that the standard error (se) is positive for all SNPs Also impute se if missing

Description

Ensure that the standard error (se) is positive for all SNPs Also impute se if missing

Usage

check_pos_se(
  sumstats_dt,
  path,
  pos_se,
  log_folder_ind,
  imputation_ind,
  check_save_out,
  tabix_index,
  nThread,
  log_files,
  impute_se
)

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.
pos_se	Binary Should the standard Error (SE) column be checked to ensure it is greater than 0? Those that are, are removed (if present in sumstats file). Default TRUE.
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.
nThread	Number of threads to use for parallel processes.
log_files	list of log file locations
impute_se	Binary, whether the standard error should be imputed using other effect data if it isn't present in the sumstats. Note that this imputation is an approximation so could have an effect on downstream analysis. Use with caution. The different methods MungeSumstats will try and impute se (in this order or priority) are: BETA / Z 2. abs(BETA/ qnorm(P/2)) Default is FALSE.

Value

list containing sumstats_dt, the modified summary statistics data table object and the log file list

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