goseq2: goseq2

In aiminy/GOSJ: A R package for GO term enrichment analysis with the flexible bias factor adjustment

Description

Modifying goseq to generate GO term with the listed DEgene

Usage

goseq2(pwf, genome, id, gene.model, gene2cat = NULL, test.cats = c("GO:CC",
  "GO:BP", "GO:MF"), method = "Wallenius", repcnt = 2000,
  use_genes_without_cat = FALSE)

Arguments

pwf:	probability weight function
genome:	genome you use
id:	which gene id
gene2cat:	a list with gene as name and category as value
test.cats:	the category you choose
method:	which method for calculting overpresentation p-value
repcnt:	the number of replications
use_genes_without_cat:	whether using genes without category or not

Examples

data(gene.model)
gene_model<-gene.model

GO.wall.DE_interest.geneGL=goseq2(Gene.based.DE.feature.based.DE$pwfGeneGL,"mm10","ensGene",gene.model=gene_model)

GO.wall.DE_interes.geneFT=goseq2(Gene.based.DE.feature.based.DE$pwfGeneFeature,"mm10","ensGene",gene.model=gene_model)

GO.wall.DE_interest.FtFT=goseq2(Gene.based.DE.feature.based.DE$pwfFeatureFeature,"mm10","ensGene",gene.model=gene_model)

aiminy/GOSJ documentation built on May 12, 2019, 3:38 a.m.