sigGene: Return significantly regulated genes

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

Return significantly regulated genes

Description

Return significantly regulated genes

Usage

sigGene(countDgeResult, contrast, value = NULL)

sigPosGene(countDgeResult, contrast, value = NULL)

sigNegGene(countDgeResult, contrast, value = NULL)

Arguments

countDgeResult	An EdgeResult object
contrast	Character, contrast(s) of interest
value	NULL or character string, if not NULL, it must be a column name in the feature annotation data.

Value

A vector of identifiers

Functions

• sigPosGene(): Only return positively significantly regulated genes

• sigNegGene(): Only return negatively significantly regulated genes

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(GeneID=1:nrow(exMat),
  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)
sigGenes(exDgeRes)
sigPosGenes(exDgeRes)
sigNegGenes(exDgeRes)
## specify the value type to return
sigGenes(exDgeRes, value="GeneSymbol")
sigPosGenes(exDgeRes, value="GeneSymbol")
sigNegGenes(exDgeRes, value="GeneSymbol")

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