cisTest-class: Class "cisTest" for storing the results of the function...

In sigaR: Statistics for Integrative Genomics Analyses in R

Description

The class cisTest is the output of a call to cisEffectTest. It stores results from a hypothesis test.

Slots

geneInfo:

Object of class "data.frame". E.g., annotation information of genes.

geneId:

Object of class "numeric". Row number in ExpressionSet-object used in {cisEffectTes}, corresponding to a gene.

comparison:

Object of class "numeric". Indicator of test performed, either "1" (loss vs. no-loss) or "2" (no-gain vs. gain).

av.prob1:

Object of class "numeric". The estimated marginal call probability.

av.prob2:

Object of class "numeric". The estimated marginal call probability.

effectSize:

Object of class "numeric". Estimated genomic cis-effect on gene expression.

R2:

Object of class "numeric". Percentage of explained variation in expression levels by .

regId:

Object of class "numeric". Indicator for the region (NULL in the regional-analysis).

beginReg:

Object of class "numeric". Row number in ExpressionSet-object corresponding to the first gene of the region (NULL in the regional-analysis).

endReg:

Object of class "numeric". Row number in ExpressionSet-object corresponding to the last gene of the region (NULL in the regional-analysis).

shrinkage:

Object of class "numeric". Amount of shrinkage applied in the regional analysis (NULL in the regional-analysis).

p.value:

Object of class "numeric". P-value for the non-parametric test of the genomic cis-effect on expression levels.

adjP.value:

Object of class "numeric". BH-multiple testing correct p-values.

analysisType

Indicator whether the test statistic has been "shrunken" within a region. Either "univariate" (no shrinkage) or "regional" (shrinkage).

testStatistic

Test statistic 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.

Methods

cisEffectTable

signature(object = "cisTest"): Prints the test results.

Author(s)

Wessel van Wieringen: [e-mail]

See Also

cisEffectTest

Examples

showClass("cisTest")

sigaR documentation built on April 28, 2020, 6:05 p.m.