rgsepd (version 1.4.2)

GSEPD_Export_DESeq: 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.

Value

• an object of class DESeqDataSet

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.

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=500,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)