cameraLimmaVoomResultsByContrast | R Documentation |
Apply the CAMERA method to a DGEList object
cameraLimmaVoomResultsByContrast(
limmaVoomResults,
index,
doParallel = FALSE,
...
)
limmaVoomResults |
A LimmaVoomResults object, with GeneSymbol available |
index |
List of integer indices of genesets, names are names of gene sets |
doParallel |
Logical, whether |
... |
Not used |
A data.frame
containing CAMERA results.
exMat <- matrix(rpois(120, 10), nrow=20, ncol=6)
exGroups <- gl(2,3, labels=c("Group1", "Group2"))
exDesign <- model.matrix(~0+exGroups)
colnames(exDesign) <- levels(exGroups)
exContrast <- matrix(c(-1,1), ncol=1, dimnames=list(c("Group1", "Group2"), c("Group2.vs.Group1")))
exDescon <- DesignContrast(exDesign, exContrast, groups=exGroups)
exFdata <- data.frame(GeneSymbol=sprintf("Gene%d", 1:nrow(exMat)))
exPdata <- data.frame(Name=sprintf("Sample%d", 1:ncol(exMat)),
Group=exGroups)
exDgeList <- DGEList(exMat, genes=exFdata, samples=exPdata)
exDgeList <- edgeR::estimateDisp(exDgeList, exDesign)
edgeObj <- EdgeObject(exDgeList, exDescon)
limmaVoomRes <- ribiosNGS::dgeWithLimmaVoom(edgeObj)
cameraLimmaVoomResultsByContrast(limmaVoomRes, index=c(1:5))
cameraLimmaVoomResultsByContrast(limmaVoomRes, index=list(GS1=1:5, GS2=6:10))
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