newGeneSets {SeqGSEA} | R Documentation

## Initialize a new SeqGeneSet object

### Description

This is an internal function to generate a new SeqGeneSet object.

### Usage

    newGeneSets(GS, GSNames, GSDescs, geneList, scGSEA = FALSE,
                name = NA_character_, sourceFile = NA_character_,
                GSSizeMin = 5, GSSizeMax = 1000)

### Arguments

`GS` | a list, each element is an integer vector, indicating the indexes of genes in each gene set. See Details below.
`GSNames` | a character string vector, each is the name of each gene set.
`GSDescs` | a character string vector, each is the description of each gene set.
`geneList` | a character string vector of gene IDs. See Details below.
`scGSEA` | logical, if this object used for scGSEA.
`name` | the name of this category of gene sets.
`sourceFile` | the source file name of this category of gene sets.
`GSSizeMin` | the minimum number of genes in a gene set to be analyzed. Default: 5
`GSSizeMax` | the maximum number of genes in a gene set to be analyzed. Default: 1000

### Details

TBA

### Value

A SeqGeneSet object.

### Author(s)

Xi Wang, xi.wang@newcastle.edu.au

### See Also

`loadGenesets`, `SeqGeneSet-class`

### Examples

    ##
    gs <- newGeneSets(GS=list(1:10, 6:15, 11:20),
                      geneList=paste("Gene", 1:22, sep=""),
                      GSNames=c("gs1","gs2","gs3"),
                      GSDescs=c("test1","test2","test3"),
                      name="gs examples")
    gs
    ## End

[Package SeqGSEA version 1.34.0 Index]