getDiffExpressedGenes: Get differentially expressed genes between tumor and normal...

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

Description

This function inherit differential gene expression analysis from "limma" package. The function creates 2 groups (normal and tumor) based on TCGA barcodes and calculate differential gene expression between groups. Finally it returns "DGEResult" object list.

Usage

getDiffExpressedGenes(dataObject, DrawPlots = TRUE)

Arguments

dataObject	: "FirehoseData" object that includes raw gene count from RNAseq platform or normalized expression values from array platfroms.
DrawPlots	: if set as "TRUE", function will draw heatmap, volcano plot and model plot from "voom" function.

Value

This function returns a list where each item will be "DGEResult" object for one comparison.

Author(s)

Mehmet Kemal Samur

Examples

data(RTCGASample)
dgegenes = getDiffExpressedGenes(a2)

RTCGAToolbox documentation built on May 2, 2019, 5:16 p.m.