FastGSEA: Fast way to do GSEA for a geneList object

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

Fast way to do GSEA for a geneList object

Usage

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<[e-mail]>

See Also

gseGO; gseKEGG; gseMKEGG

Examples

#'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.