gseGO2 {signatureSearch} | R Documentation

## Modified GSEA with GO Terms

### Description

This modified Gene Set Enrichment Analysis (GSEA) of GO terms supports gene test sets with large numbers of zeros.

### Usage

    gseGO2(
      geneList,
      ont = "BP",
      OrgDb,
      keyType = "SYMBOL",
      exponent = 1,
      nproc = 1,
      nPerm = 1000,
      minGSSize = 2,
      maxGSSize = 500,
      pvalueCutoff = 0.05,
      pAdjustMethod = "BH",
      verbose = TRUE
    )

### Arguments

`geneList` | named numeric vector with gene SYMBOLs in the name slot decreasingly ranked by scores in the data slot.
`ont` | one of "BP", "MF", "CC" or "ALL"
`OrgDb` | OrgDb, e.g., "org.Hs.eg.db".
`keyType` | keytype of gene
`exponent` | weight of each step
`nproc` | if not equal to zero, sets `BPPARAM` to use `nproc` workers (default = 1)
`nPerm` | permutation numbers
`minGSSize` | integer, minimum size of each gene set in annotation system
`maxGSSize` | integer, maximum size of each gene set in annotation system
`pvalueCutoff` | pvalue cutoff
`pAdjustMethod` | pvalue adjustment method
`verbose` | print message or not

### Value

feaResult object

### Examples

    data(targetList)
    # gsego <- gseGO2(geneList=targetList, ont="MF", OrgDb="org.Hs.eg.db",
    #                 pvalueCutoff=1)
    # head(gsego)

[Package signatureSearch version 1.0.4 Index]