cameraDGEListByContrast: Apply the CAMERA method to a DGEList object and a contrast

In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

Apply the CAMERA method to a DGEList object and a contrast

Description

Apply the CAMERA method to a DGEList object and a contrast

Usage

cameraDGEListByContrast(dgeList, index, design, contrasts, doParallel = FALSE)

Arguments

dgeList	A DGEList object, with GeneSymbol available, and dispersion must be estimated
index	List of integer indices of genesets, names are names of gene sets
design	Design matrix
contrasts	Contrast matrix
doParallel	Logical, whether parallel::mclapply should be used. Since at the current setting it makes a job running forever, use TRUE only if you are debugging the code.

Examples

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)
cameraDGEListByContrast(exDgeList, index=1:5, design=exDesign, contrasts=exContrast)
cameraDGEListByContrast(exDgeList, 
  index=list(1:5, 6:10),
  design=exDesign, contrasts=exContrast)
  

bedapub/ribiosGSEA documentation built on March 30, 2023, 3:26 p.m.