cisEffectTest {sigaR} | R Documentation |
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.
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 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 |
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: w.vanwieringen@vumc.nl
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.
matchAnn2Ann
, cisEffectTune
, cisEffectTable
, cisEffectPlot
# 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)