RTCGA (version 1.2.2)

getDiffExpressedGenes: Perform differential gene expression analysis for mRNA expression data.

Description

getDiffExpressedGenes returns a list that stores the results for each dataset.

Usage

getDiffExpressedGenes(dataObject, DrawPlots = TRUE, adj.method = "BH",
  adj.pval = 0.05, raw.pval = 0.05, logFC = 2, hmTopUpN = 100,
  hmTopDownN = 100, meanFilter = 10)

Arguments

dataObject

This must be FirehoseData object.

DrawPlots

A logical parameter to draw heatmaps and volcano plots.

adj.method

Raw p value adjustment methods (Default "BH")

adj.pval

Adjusted p value cut off for results table (Default 0.05)

raw.pval

raw p value cut off for results table (Default 0.05)

logFC

log fold change cut off for results table (Default 2)

hmTopUpN

Max number of up regulated genes in heatmap (Default 100)

hmTopDownN

Max number of down regulated genes in heatmap (Default 100)

meanFilter

Mean read counts for each gene to filter not expressed genes (Default 10)

Value

• Returns a list that stores results for each dataset

Examples

data(RTCGASample)
dgegenes = getDiffExpressedGenes(RTCGASample)
dgegenes
showResults(dgegenes[[1]])
dgegenes = showResults(dgegenes[[1]])
head(dgegenes)