check_save_path: Check if save path and log folder is appropriate

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Check if save path and log folder is appropriate

Description

Check if save path and log folder is appropriate

Usage

check_save_path(
  save_path,
  log_folder,
  log_folder_ind,
  tabix_index,
  write_vcf = FALSE,
  verbose = TRUE
)

Arguments

save_path	File path to save formatted data. Defaults to tempfile(fileext=".tsv.gz").
log_folder	Filepath to the directory for the log files and the log of MungeSumstats messages to be stored. Default is a temporary directory. Note the name of the log files (log messages and log outputs) are now the same as the name of the file specified in the save path parameter with the extension '_log_msg.txt' and '_log_output.txt' respectively.
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.
write_vcf	Whether to write as VCF (TRUE) or tabular file (FALSE).
verbose	Print messages.

Value

Corrected save_path, the file type, the separator, corrected log_folder,the log file extension.

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.