FastGSEA: Fast way to do GSEA for a geneList object

Description Usage Arguments Author(s) See Also Examples

View source: R/BI_FastGSEA.R

Description

Fast way to do GSEA for a geneList object

Usage

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FastGSEA(geneList, OrgDb = NULL, keyType = NULL,
  pvalueCutoff = list(gseGO = 0.01, gseKEGG = 0.01, gseMKEGG = 0.01),
  verbose = T, save.path = "GSEA", names = "love")

Arguments

geneList

a numeric with id names.For example,logFoldChang with ENSEMBL id names.Note that the names of geneList must be the same type of genes

OrgDb

OrgDb dataset.If NULL,use "org.Hs.eg.db"

keyType

the type of gene.Support automatically test

pvalueCutoff

a list of pvalue adjust method for gseGO,gseKEGG and gseMKEGG.Note that the default value is 0.01,you can set 0.05 if you want a robust exploration.

verbose

LuckyVerbose gseplot running message or not

save.path

the sub path of saved files

names

the main path and part names of saved files

Author(s)

Weibin Huang<654751191@qq.com>

See Also

gseGO; gseKEGG; gseMKEGG

Examples

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#'import org.Hs.eg.db
data(geneList, package = "DOSE")
gsea <- FastGSEA(geneList,
                 OrgDb = NULL,
                 keyType = NULL,
                 pvalueCutoff = list(gseGO=0.05,
                                     gseKEGG = 0.05,
                                     gseMKEGG = 0.05),
                 verbose = T,
                 save.path = "GSEA",
                 names = "love")

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.