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. -
--pi-zero
Estimate the percentage of the observed p-values that are drawn according to the null hypothesis (known as pi0 in the statistics literature), and include this percentage in the FDR calculation. By default, a fixed pi-zero of 1 is used. -
--pi-zero-file <file>
Print the estimated value of pi-zero in the given file. This option implies the--pi-zero
option as well. -
--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 <int>
Set the seed for the random number generator. By default, the seed is set from the clock. -
--verbosity 0|1|2|3|4
Set the verbosity of output to stderr. Default=2.
Warning messages: None
Bugs:
None known.