FastMS: Fast Molecular Signatures Analysis via clusterProfilter

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

Description

Fast Molecular Signatures Analysis via clusterProfilter

Usage

FastMS(genes, geneList, default.universe = T, pAdjustMethod = "BH",
  pvalueCutoff = list(enrichMS = 0.05, gseMS = 0.05),
  qvalueCutoff = 0.2, cnet.showCategory = 5, verbose = TRUE,
  save.path = "Molecular Signatures", names = "love")

Arguments

genes	a character of genes.The ENSEMBL id is the best.Note that no replicate should exist.
geneList	a named numeric of genes.The ENSEMBL id is the best.Note that no replicate should exist.
default.universe	whether to use default universe.If default.universe = F,the background genes would be provide by geneList
pAdjustMethod	the mathod of pvalue adjustment
pvalueCutoff	a list of pvalue adjust method for enricher and GSEA
qvalueCutoff	cutoff of q value
cnet.showCategory	the number of showed cluster at cnetplot
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

enricher; GSEA

Examples

data(geneList, package = "DOSE")
genes = names(geneList)[1:100]
geneList = geneList
ms <- FastMS(genes,
             geneList,
             pAdjustMethod = "BH",
             pvalueCutoff = list(enrichMS=0.00001,
                                 gseMS = 0.00001),
             qvalueCutoff  = 0.2,
             cnet.showCategory = 5,
             verbose = TRUE,
             save.path = "Molecular Signatures",
             names = "love")

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