GSEPD_Process: Processing

In kstammits/rgsepd: Gene Set Enrichment / Projection Displays

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
 

kstammits/rgsepd documentation built on Oct. 13, 2022, 6:43 p.m.