GSEPD_PullDEG {rgsepd} | R Documentation

## Pull Differentially Expressed Genes

### Description

After processing, if you want to easily access the differentially expressed transcript listing, this function will read in the default generated files, and apply filters as specified by the GSEPD master object (default p-values).

### Usage

    GSEPD_PullDEG(GSEPD, PTHRESH)

### Arguments

`GSEPD` | The master object should have been processed already such that differentially expressed genes are readily available.
`PTHRESH` | Specify the degree of stringency.

### Value

Returns a vector of ID#, suitable to row-subsetting of the finalCounts table.

### 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

      Significant_Genes <- GSEPD_PullDEG(G, PTHRESH=0.0250)
      #then do more with these identifiers:
      print(Significant_Genes)
      # GSEPD_Heatmap(G, genes= Significant_Genes )

[Package rgsepd version 1.18.0 Index]