newGeneSets: Initialize a new SeqGeneSet object

In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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, [e-mail]

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 

SeqGSEA documentation built on Nov. 8, 2020, 5:46 p.m.