A wrapper for some of the functionality for the multtest
package. It also includes hooks to calculate qvalues with John
D. Storey's ‘qvalue.R’ code.
1  mt.wrapper(proc, X, classlabel, test="t", rawpcalc="Parametric", side="abs", ...)

proc 
A character string containing the name of the multiple
testing procedure for which adjusted pvalues are to be
computed. This vector should include any of the following:

X 
A data frame or matrix, with m rows corresponding to variables
(hypotheses) and
n columns to observations. In the case of gene expression data, rows
correspond to genes and columns to mRNA samples. The data can
be read using 
classlabel 
A vector of integers corresponding to observation (column)
class labels. For k classes, the labels must be integers
between 0 and k1. For the 
test 
A character string specifying the statistic to be
used to test the null hypothesis of no association between the
variables and the class labels. 
rawpcalc 
A character string specifying how to calculate
nominal/raw pvalues. The possible choices are 
side 
A character string specifying the type of rejection region. 
... 
Further arguments for 
A data frame with components
index 
Vector of row indices, between 1 and 
teststat 
Vector of test statistics, ordered according to

rawp 
Vector of raw (unadjusted) pvalues, ordered
according to 
adjp 
Vector of adjusted pvalues, ordered according to

plower 
For 
Colin A. Smith webbioc@colinsmith.org
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