Difference between revisions of "Shore mtc"
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* Benjamini-Yekutieli false discovery rate control (fdr_by). | * Benjamini-Yekutieli false discovery rate control (fdr_by). | ||
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'''Usage:''' shore mtc [OPTIONS] | '''Usage:''' shore mtc [OPTIONS] | ||
Latest revision as of 10:06, 28 September 2011
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 | |
