FastMS: Fast Molecular Signatures Analysis via clusterProfilter

In huangwb8/lucky: 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 = 0.1, 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
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

Details

More about MsigDB & GSEA: http://software.broadinstitute.org/gsea/msigdb/index.jsp

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")

huangwb8/lucky documentation built on Oct. 16, 2019, 9:01 a.m.