Shore mtc

The subprogram shore mtc implements various multiple testing correction methods. The expected input is a tab-delimited text file with a header, and the column containing the p-values to be adjusted must be named raw_p.

Implemented methods include

• Benjamini-Hochberg false discovery rate control (fdr_bh)
• Bonferroni familywise error rate control (fwer_bonferroni)
• Holm familywise error rate control (fwer_holm)
• Hochberg familywise error rate control (fwer_hochberg)
• Sidak singlestep familywise error rate control (fwer_sidak_ss)
• Sidak stepdown familywise error rate control (fwer_sidak_sd)
• Benjamini-Yekutieli false discovery rate control (fdr_by).

Command line options

Usage: shore mtc [OPTIONS]

Mandatory
-m, --method=<arg[,...]>		Select correction method(s), out of: fdr_bh, fwer_bonferroni, fwer_holm, fwer_hochberg, fwer_sidak_ss, fwer_sidak_sd, fdr_by
-i, --input-file=<arg>	(Default: stdin)	The file the raw p-values are read from (expects a column 'raw_p')
-o, --output-file=<arg>	(Default: stdout)	Output file
Output
-u, --fdr-max=<arg>	(Default: 1)	Maximum q-value to report
-e, --echo-comments		Echo all comments read from input files to stdout
-q, --quiet		Do not print input, only report the q-values
Other
-j, --input-header=<arg[,...]>		Use arg as input file header