GSEPD_Export_DESeq {rgsepd} | R Documentation

## Export DESeqDataSet object

### Description

Converts from the internal matrices to a DESeq standard object.

### Usage

    GSEPD_Export_DESeq(G)

### Arguments

`G` | The GSEPD list object to extract a DeseqDataSet from.

### Details

Using the given GSEPD object's finalCounts and sampleMeta, a simple DESeqDataSet object is created with the default design matrix. Provided for interoperability with other analysis packages.

### Value

an object of class DESeqDataSet

### References

DESeq2

### 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!
      dds <- GSEPD_Export_DESeq(G)
      print(dds)

[Package rgsepd version 1.19.1 Index]