mt.wrapper {webbioc} | R Documentation |
A wrapper for some of the functionality for the multtest
package. It also includes hooks to calculate q-values with John
D. Storey's ‘q-value.R’ code.
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 p-values 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 k-1. 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 p-values. 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) p-values, ordered
according to |
adjp |
Vector of adjusted p-values, ordered according to
|
plower |
For |
Colin A. Smith webbioc@colinsmith.org