setup_GSEA {InPAS} | R Documentation

## prepare files for GSEA analysis

### Description

output the log2 transformed delta PDUI txt file, chip file, rank file and phynotype label file for GSEA analysis

### Usage

    setup_GSEA(
      eset,
      groupList,
      outdir,
      preranked = TRUE,
      rankBy = c("logFC", "P.value"),
      rnkFilename = "InPAS.rnk",
      chipFilename = "InPAS.chip",
      dataFilename = "dPDUI.txt",
      PhenFilename = "group.cls"
    )

### Arguments

`eset` | A UTR3eSet object, output of `test_dPDUI()`
`groupList` | A list of grouped sample tag names, with the group names as the list's name, such as list(groupA = c("sample_1", "sample_2", "sample_3"), groupB = c("sample_4", "sample_5", "sample_6"))
`outdir` | A character(1) vector, a path with write permission for storing the files for GSEA analysis. If it doesn't exist, it will be created.
`preranked` | A logical(1) vector, out preranked or not
`rankBy` | A character(1) vector, indicating how the gene list is ranked. It can be "logFC" or "P.value".
`rnkFilename` | A character(1) vector, specifying a filename for the preranked file
`chipFilename` | A character(1) vector, specifying a filename for the chip file
`dataFilename` | A character(1) vector, specifying a filename for the dataset file
`PhenFilename` | A character(1) vector, specifying a filename for the file containing samples' phenotype labels

### Author(s)

Jianhong Ou, Haibo Liu

### See Also

data formats for GSEA. https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

### Examples

    if (interactive()) {
      file <- system.file("extdata", "eset.MAQC.rda", package = "InPAS")
      load(file)
      gp1 <- c("Brain.auto", "Brain.phiX")
      gp2 <- c("UHR.auto", "UHR.phiX")
      groupList <- list(Brain = gp1, UHR = gp2)
      prepare4GSEA(eset,
                   groupList = groupList,
                   outdir = tempdir(),
                   preranked = TRUE,
                   rankBy = "logFC")
    }

[Package InPAS version 2.2.0 Index]