EdgeObject: Construct an EdgeObject object by a count matrix and...

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Construct an EdgeObject object by a count matrix and DesignContrast

Description

Construct an EdgeObject object by a count matrix and DesignContrast

Usage

EdgeObject(object, designContrast, ...)

Arguments

object	A matrix containing counts of features
designContrast	A DesignContrast object
...	Other parameters

Examples

exMat <- matrix(rpois(120, 10), nrow=20, ncol=6)
exGroups <- gl(2,3, labels=c("Group1", "Group2"))
exDesign <- model.matrix(~0+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(Identifier=sprintf("Gene%d", 1:nrow(exMat)))
exPdata <- data.frame(Name=sprintf("Sample%d", 1:ncol(exMat)),
                     Group=exGroups)
exObj <- EdgeObject(exMat, exDescon)
exObj2 <- EdgeObject(exMat, exDescon, fData=exFdata)
exObj3 <- EdgeObject(exMat, exDescon, 
                     fData=exFdata, pData=exPdata)
            
fData(exObj3)

dgeList <- edgeR::DGEList(counts=exMat, samples=exPdata, genes=exFdata)
exObj4 <- EdgeObject(dgeList, exDescon)

## note that pData are appended after count information
pData(exObj2)
pData(exObj3)

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.