qvalue

Usage: qvalue [options] <pvalues>

Description:

Takes as input a list of p-values and prints a corresponding list of q-values, computed using the method of Benjamini and Hochberg (Journal of the Royal Statistical Society B, 57:289-300, 1995).

Input:

The input file contains one p-value per line. The p-values do not have to be in sorted order.

Output:

The output is two tab-delimited columns, p-value and q-value, sorted by p-value.

Options:

• --null <file> Treat the primary input file as raw scores, and begin by estimating p-values from the empirical null scores given in this file. The --header and --column arguments apply to this file as well as the primary input file.
• --fdr Only compute FDR estimates.
• --bootstraps <int> Number of bootstraps to perform when estimating pi-zero. Default=1000.
• --header <int> Skip the specified number of lines at the beginning of the given file. Default=0.
• --column <int> Read the p-value from the specified tab-delimited column number. Columns are indexed starting from 1. Default=1.
• --append Print the input file to stdout, with an additional, tab-delimited column containing the q-value.
• --seed <n> - Seed for random number generator.
• --verbosity 1|2|3|4 - Set the verbosity of status reports to standard error. The default level is 2.

Warning messages: None

Bugs:

None known.