GSEPD_Process {rgsepd} | R Documentation

## Processing

### Description

Primary interface, use this function to kick off the pipeline.

### Usage

    GSEPD_Process(GSEPD)

### Arguments

`GSEPD` | The initialized GSEPD master object to operate on.

### Details

Runs the pipeline. If any files are already present matching the generated filenames, they will be reused. If you changed a parameter that would alter the generated filenames, new ones are created. If a customization parameter is not part of the filename (like a p-value cutoff), you should change the output folder to keep new files separate.

### Value

Returns the GSEPD object post-processed, for use in further plotting functions. Optional.

### See Also

GSEPD_INIT

### 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 ) #would run DESeq2 and GOSeq and GSEPD comparing conditions A and B

[Package rgsepd version 1.20.2 Index]