GSEPD_DEGHeatmap {rgsepd} | R Documentation

## Differentially Expressed Genes Heatmap

### Description

Generates a gene-by-subject heatmap plot of differentially expressed genes.

### Usage

     GSEPD_DEGHeatmap(G)

### Arguments

`G` | The GSEPD master object carries sample information and gene expression data. It should have already run Process() to be eligible. Parameters regarding differential expression limits are set within the G$LIMIT list object.

### Details

After GSEPD_Process() has created differential expression tables with known filenames, this function can read those tables and make heatmap plots for a subset of genes. We use the N most significant genes, specified by the `MAX_Genes_for_Heatmap` parameter of the passed GSEPD object.

### Value

This function doesn't return anything. If successful, four PDF files are created. HM and HM- are all subjects from sampleMeta and finalCounts, HMS and HMS- are only those in the test groups. The hyphen indicates a smaller unlabeled figure. In each case the data is manipulated as in `GSEPD_Heatmap()` such that complete linkage clustering is performed on z-score normalized genes using the normalized counts directly from DESeq2::varianceStabilizingTransformation, which are displayed in the labeled figures.

### Examples

      data("IlluminaBodymap")
      data("IlluminaBodymapMeta")
      set.seed(1000) #fixed randomness
      isoform_ids <- Name_to_RefSeq(c("HIF1A","EGFR","MYH7","CD33","BRCA2"))
      rows_of_interest <- unique( c( isoform_ids ,
                                     sample(rownames(IlluminaBodymap),
                                            size=2000,replace=FALSE)))
      G <- GSEPD_INIT(Output_Folder="OUT",
                    finalCounts=round(IlluminaBodymap[rows_of_interest , ]),
                    sampleMeta=IlluminaBodymapMeta,
                    COLORS=c("green","black","red"))
      G <- GSEPD_ChangeConditions( G, c("A","B")) #set testing groups first!
      G <- GSEPD_Process( G ) #have to have processed results to plot them
      GSEPD_DEGHeatmap(G) # all parameters automatic

[Package rgsepd version 1.16.0 Index]