GSEPD_ChangeOutput {rgsepd} | R Documentation

## 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.

### Author(s)

karl.stamm@gmail.com

### 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

[Package rgsepd version 1.14.1 Index]