Description
Usage
Arguments
Value
Author(s)
View source: R/multtest.R
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.
 (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:
"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 k1. 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 k1.

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 twosample Welch tstatistics
(unequal variances).
If test="t.equalvar" , the tests are based on twosample
tstatistics with equal variance for the two samples. The
square of the tstatistic is equal to an Fstatistic for k=2.
If test="wilcoxon" , the tests are based on standardized rank sum Wilcoxon statistics.
If test="f" , the tests are based on Fstatistics.
If test="pairt" , the tests are based on paired tstatistics. The
square of the paired tstatistic is equal to a block Fstatistic for k=2.
If test="blockf" , the tests are based on Fstatistics which
adjust for block differences
(cf. twoway analysis of variance).

rawpcalc 
A character string specifying how to calculate
nominal/raw pvalues. The possible choices are "Parametric"
or "Permutation" .

side 
A character string specifying the type of rejection region.
If side="abs" , twotailed tests, the null hypothesis is rejected for large absolute values of the test statistic.
If side="upper" , onetailed tests, the null hypothesis is rejected for large values of the test statistic.
If side="lower" , onetailed 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
pvalues, next their unadjusted pvalues, 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) pvalues, ordered
according to index .

adjp 
Vector of adjusted pvalues, ordered according to
index .

plower 
For mt.minP function
only, vector of "adjusted pvalues", where ties in the permutation
distribution of the successive minima of raw pvalues
with the observed pvalues 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
webbioc documentation built on May 20, 2017, 9:47 p.m.
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