newGeneSets: Initialize a new SeqGeneSet object

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/Allclasses.R

Description

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

Usage

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newGeneSets(GS, GSNames, GSDescs, geneList, 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.

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

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##
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 


SeqGSEA documentation built on May 20, 2017, 10:46 p.m.
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