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:
"Bonferroni" , "Holm" , "Hochberg" ,
"SidakSS" , "SidakSD" , "BH" , "BY" ,
"maxT" , "minP" , "q" .
|
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 read.table .
|
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 blockf test option,
observations may be divided into
n/k blocks of k observations each. The observations are
ordered by block, and within each block, they are labeled using the
integers 0 to k-1.
|
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. If test="t" , the tests are based on two-sample Welch t-statistics
(unequal variances). If test="t.equalvar" , the tests are based on two-sample
t-statistics with equal variance for the two samples. The
square of the t-statistic is equal to an F-statistic for k=2. If test="wilcoxon" , the tests are based on standardized rank sum Wilcoxon statistics.If test="f" , the tests are based on F-statistics.If test="pairt" , the tests are based on paired t-statistics. The
square of the paired t-statistic is equal to a block F-statistic for k=2. If test="blockf" , the tests are based on F-statistics which
adjust for block differences
(cf. two-way analysis of variance).
|
rawpcalc |
A character string specifying how to calculate
nominal/raw p-values. The possible choices are "Parametric"
or "Permutation" .
|
side |
A character string specifying the type of rejection region. If side="abs" , two-tailed tests, the null hypothesis is rejected for large absolute values of the test statistic.If side="upper" , one-tailed tests, the null hypothesis is rejected for large values of the test statistic.If side="lower" , one-tailed tests, the null hypothesis is rejected for small values of the test statistic.
|
... |
Further arguments for mt.maxT , mt.minP , qvalue . |
A data frame with components
index |
Vector of row indices, between 1 and nrow(X) ,
where rows are sorted first according to their adjusted
p-values, next their unadjusted p-values, and
finally their test statistics. |
teststat |
Vector of test statistics, ordered according to
index . To get the test statistics in the original data
order, use teststat[order(index)] . |
rawp |
Vector of raw (unadjusted) p-values, ordered according to index . |
adjp |
Vector of adjusted p-values, ordered according to index . |
plower |
For mt.minP function only, vector of
"adjusted p-values", where ties in the permutation
distribution of the successive minima of raw p-values
with the observed p-values are counted only once. Note
that procedures based on plower do not control the FWER.
Comparison of plower and adjp gives an idea of
the discreteness of the permutation distribution. Values in
plower are ordered according to index . |
Colin A. Smith webbioc@colinsmith.org