getDiffExpressedGenes {RTCGAToolbox} | R Documentation

## 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)

[Package RTCGAToolbox version 2.16.3 Index]