save_log: Log entries for QC_GWAS

In QCGWAS: Quality Control of Genome Wide Association Study Results

Log entries for QC_GWAS

Description

A subroutine for reporting problems encountered while running QC_GWAS. It's not designed for use outside of this context, so we recommend that users do not bother with it. It is described here for the sake of completeness only.

Usage

save_log(phaseL, checkL, typeL, SNPL = allSNPs,
         allSNPs = 1L, actionL, noteL = "", fileL)

Arguments

phaseL, checkL, typeL	character-strings indicating (very briefly) what occurred to trigger a log entry.
SNPL	integer value indicating the number of SNPs affected.
allSNPs	integer value indicating the total number of SNPs in the dataset.
actionL	character-string describing very briefly the response to situation.
noteL	character-string for longer explanations of what happened.
fileL	character-string of the directory path and the file name, without file extension, of the log file.

Details

save_log is used to add entries to the log file the moment they are triggered (as opposed to waiting until the QC concludes and then saving the entire log). In case of a fatal crash, the log file should therefor give some indication of where in the QC it occurred.

save_log does not create the log file (this is done by QC_GWAS): it merely appends entries to the bottom of the specified file, regardless of what that file is. Hence it is not recommended to use the function outside of QC_GWAS.

Value

save_log returns an invisible NULL. The relevant output is the entry added to the log file.

QCGWAS documentation built on May 30, 2022, 5:05 p.m.