qvalue [options] <pvalues file>
Takes as input a list of pvalues and prints a corresponding list of qvalues, computed using the method of Benjamini and Hochberg (Journal of the Royal Statistical Society B, 57:289300, 1995).
The name of a tab separated file containing a column of pvalues. Other columns may exist. If the name is  then the input data is read from standard input.
Outputs tabdelimited columns. If the append option is given, then the line from the input is listed first, followed by the pvalue (only when null is specified) and qvalue. Otherwise it outputs the raw score (only when null is specified). followed by the pvalue and qvalue. The lines are sorted by pvalue.
Option  Parameter  Description  Default Behaviour 

General Options  
null  file  Treat the primary input file as raw scores, and begin by estimating pvalues 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.  The primary input is assumed to actually contain pvalues. 
goodscore  highlow  Choose low if smaller scores are better or high if larger scores are better.  Smaller scores are considered better. 
pizero  Estimate the fraction (pizero) of the empirical distribution that is
drawn according to the null hypothesis. This uses the
method described in:
John Storey, "A direct approach to false discovery rates",
Journal of the Royal Statistical Society B, 64:3, 479498,
2002.

The estimation step is skipped and the program conservatively sets pizero to 100%.  
pizerofile  file name  Specify a file to store the pizero estimate in. This option implies the pizero option.  The results of the pizero estimate (if calculated) are not stored in a file. 
fdr  Only compute false discovery rate (FDR) estimates.  The FDR values are converted into qvalues.  
bootstraps  num  Number of bootstraps to perform when estimating pizero.  The program performs 1000 bootstraps. 
header  line count  Treat the first line count lines of the pvalues file as the header. If the append option is specified these lines will also be included in the output.  No lines are treated as headers. 
column  column number  Read the pvalue from the specified column number. The first column is 1, the second column is 2 and so on...  The pvalue is read from the first column. 
append  Print all the columns in the input file to standard output with additional pvalue (raw scores only) and qvalue columns.  Print the raw score (only when raw scores are supplied), pvalue and qvalue in tab separated columns.  
seed  seed  Set the seed value for the pseudorandom number generator.  The seed value is set from the system clock. 