rgsepd (version 1.2.0)

GSEPD_ChangeOutput: GSEPD_ChangeOutput

Description

Update the stored output folder designation, and create it if necessary. This is useful if you want to change some LIMIT parameters and re-run the pipeline. Don't forget to GSEPD_Process() after changing settings.

Usage

GSEPD_ChangeOutput(GSEPD, newFolder)

Arguments

GSEPD

The initial GSEPD parameter object to update the output folder of.

newFolder

The new output folder to be created.

Value

Returns the updated GSEPD parameter object.

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!           

  G<- GSEPD_ChangeOutput(G, "Output2")
  #G <- GSEPD_Process( G ) #would output to folder Output2
  #now tweak some settings and re-do
  G$LIMIT$LFC <- 0.25 #lower than default log-fold-change limit
  G<- GSEPD_ChangeOutput(G, "Output-Low")
  #G <- GSEPD_Process( G ) #would output to folder Output-Low