Reads the output files produced by the DENTIST C++ software and returns
a structured data frame. Useful for comparing DENTIST output against
dentist_from_files results.
Usage
parse_dentist_output(output_prefix, pValueThreshold = 5e-08)
Arguments
- output_prefix
The output prefix used when running the DENTIST software
(the --out argument).
- pValueThreshold
P-value threshold used to determine outlier status.
Default is 5e-8.
Value
A data frame with columns: SNP, test_stat, neg_log10_p, is_duplicate, outlier.
Details
The DENTIST software (non-debug mode) writes a .DENTIST.full.txt file with
4 tab-separated columns (no header): rsID, stat/lambda, -log10(pvalue), isDuplicate.
It also writes a .DENTIST.short.txt file listing outlier SNP IDs (one per line).