cisEffectTest: Nonparametric testing for copy number induced differential gene expression.

Description

A nonparametric test for the detection of copy number induced differential gene expression. The test incorporates the uncertainty of the calling of genomic aberrations: weighted version of well-known test statistics are used. An efficient permutation re-sampling procedure is used for p-value calculation. The test statistics may be "shrunken" to borrow information across neighboring genes that share the same copy number signature.

Usage

cisEffectTest(CNdata, GEdata, genes2test=NULL, GEchr, 
analysisType="univariate", testStatistic="wcvm", 
nPerm = 10000, lowCiThres = 0.1, verbose=TRUE)

Arguments

CNdata

Object of class cghCall, containing (among others) annotion and call probabilities. Features should be matched with those of the accompanying ExpressionSet-object (as may be done using the matchAnn2Ann-function).

GEdata

Object of class ExpressionSet. Features should be matched with those of the accompanying cghCall-object (as may be done using the matchAnn2Ann-function).

genes2test

Numeric indicator vector containing row number of genes for which the DNA copy number cis-effect should be tested. The function cisEffectTune yields an optimal selection.

GEchr

Column in the slot featureData of the ExpressionSet-object GEdata specifying the chromosome information of the features.

analysisType

Indicator to determine whether the test statistic should be "shrunken" within a region. Either "univariate" (no shrinkage) or "regional" (shrinkage).

testStatistic

Test statistic to be used, either "wcvm" or "wmw", the weighted Cramer-Von Mises and the weighted Mann-Whitney test statistic, respectively.

nPerm

Number of permutations used for the p-value calculation.

lowCiThres

A value between 0 and 1. Determines speed of efficient p-value calculation. Genes with a probability smaller than 0.001 of a p-value smaller than eff.p.val.thres are discarded from the permutation analysis and their p-value is set equal to 1. Should be chosen in accordance with the FDR-threshold for significance.

verbose

Logical indicator: should intermediate output be printed on the screen?

Value

Object of class cisTest.

References

Van Wieringen, W.N., Van de Wiel, M.A. (2009), "Non-parametric testing for DNA copy number induced differential mRNA gene expression", Biometrics, 65(1), 19-29.

Examples

Run this code

# load data
data(pollackCN16)
data(pollackGE16)

# test cis-effect of DNA copy number on gene expression levels
cisRes <- cisEffectTest(pollackCN16, pollackGE16, 1:nrow(pollackGE16), 1, nPerm=25)