Description Usage Arguments Value Note Author(s) References See Also Examples
View source: R/cisEffectFunctions.R
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 wellknown test statistics are used. An efficient permutation resampling procedure is used for pvalue calculation. The test statistics may be "shrunken" to borrow information across neighboring genes that share the same copy number signature.
1 2 3  cisEffectTest(CNdata, GEdata, genes2test=NULL, GEchr,
analysisType="univariate", testStatistic="wcvm",
nPerm = 10000, lowCiThres = 0.1, verbose=TRUE)

CNdata 
Object of class 
GEdata 
Object of class 
genes2test 

GEchr 
Column in the slot 
analysisType 
Indicator to determine whether the test statistic should be "shrunken" within a region. Either 
testStatistic 
Test statistic to be used, either 
nPerm 
Number of permutations used for the pvalue calculation. 
lowCiThres 
A value between 0 and 1. Determines speed of efficient pvalue calculation.
Genes with a probability smaller than 0.001 of a pvalue smaller than 
verbose 
Logical indicator: should intermediate output be printed on the screen? 
Object of class cisTest
.
This function is a rewritten version of the intCNGEan.test
function of the intCNGEan
package.
Wessel N. van Wieringen: [email protected]
Van Wieringen, W.N., Van de Wiel, M.A. (2009), "Nonparametric testing for DNA copy number induced differential mRNA gene expression", Biometrics, 65(1), 1929.
matchAnn2Ann
, cisEffectTune
, cisEffectTable
, cisEffectPlot
1 2 3 4 5 6  # load data
data(pollackCN16)
data(pollackGE16)
# test ciseffect of DNA copy number on gene expression levels
cisRes < cisEffectTest(pollackCN16, pollackGE16, 1:nrow(pollackGE16), 1, nPerm=25)

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