mergeDGEList: Merge two DGEList objects into one

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

Merge two DGEList objects into one

Description

Merge two DGEList objects into one

Usage

mergeDGEList(firstDgeList, secondDgeList, DGEListLabels = NULL)

Arguments

firstDgeList	First DGEList object
secondDgeList	Second DGELIst object
DGEListLabels	Labels, either NULL or a vector of character strings with length two The function merges two DGEList objects. It does essentially three things: Feature annotationIt extracts the common features from both objects, and use the feature annotation in the firstDgeList object as the annotation for the final object. Sample annotationIt extracts the common columns from sample annotation of both objects, and row-bind them as the annotaiton for the final object. countsMatching final features and samples, the counts matrices are column-binded. In case DGEListLabels is available, its values will be turned into a factor vector, and appended as the column DGEListLabel in the samples object of the returned value.

Examples

y1 <- matrix(rnbinom(1000, mu=5, size=2), ncol=4)
genes1 <- data.frame(GeneSymbol=sprintf("Gene%d", 1:nrow(y1)))
rownames(y1) <- rownames(genes1) <- 1:nrow(y1)
anno1 <- data.frame(treatment=gl(2,2, labels=c("ctrl", "tmt")),
    donor=factor(rep(c(1,2), each=2)))
d1 <- DGEList(counts=y1, genes=genes1, samples=anno1)

y2 <- matrix(rnbinom(1000, mu=5, size=2), ncol=4)
genes2 <- data.frame(GeneSymbol=sprintf("Gene%d", 1:nrow(y2)+100))
rownames(y2) <- rownames(genes1) <- 1:nrow(y2)+100
anno2 <- data.frame(treatment=gl(2,2, labels=c("ctrl", "tmt")),
    sex=factor(rep(c("m", "f"), each=2)))
d2 <- DGEList(counts=y2, genes=genes2, samples=anno2)

md <- mergeDGEList(d1, d2)
md2 <- mergeDGEList(d1, d2, DGEListLabels=c("d1", "d2"))

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