sigGeneDgeTable: Return dgeTable containing significantly regulated genes in...

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

Return dgeTable containing significantly regulated genes in respective contrasts

Description

Return dgeTable containing significantly regulated genes in respective contrasts

Usage

sigGeneDgeTable(countDgeResult, value = "FeatrueName")

Arguments

countDgeResult	An EdgeResult object
value	A character string, it must be a column name in the feature annotation data. Default: FeatureName.

Value

A data.frame containing dgeTable of positively and negatively regulated genes in respective contrasts

Examples

exMat <- matrix(rpois(120, 10), nrow=20, ncol=6)
exMat[2:4, 4:6] <- exMat[2:4, 4:6]+20
exMat[7:9, 1:3] <- exMat[7:9, 1:3]+20
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)
exObj <- EdgeObject(exMat, exDescon, 
                   fData=exFdata, pData=exPdata)
exDgeRes <- dgeWithEdgeR(exObj)
sigGeneDgeTable(exDgeRes, value="GeneSymbol")

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