richLevel,ANY,Annot-method | R Documentation |
Pathway Enrichment analysis for different level function
## S4 method for signature 'ANY,Annot'
richLevel(
x,
kodata,
level = "Level2",
pvalue = 0.05,
padj = NULL,
organism = NULL,
keytype = "SYMBOL",
ontology = "",
minSize = 2,
maxSize = 500,
keepRich = TRUE,
filename = NULL,
padj.method = "BH",
sep = ","
)
x |
vector contains gene names or dataframe with DEGs information |
kodata |
KEGG annotation data |
pvalue |
cutoff pvalue |
padj |
cutoff p adjust value |
organism |
organism |
keytype |
keytype for input genes |
ontology |
ontology type |
minSize |
minimal number of genes included in significant terms |
maxSize |
maximum number of genes included in significant terms |
keepRich |
keep terms with rich factor value equal 1 or not (default: TRUE) |
filename |
output filename |
padj.method |
pvalue adjust method(default:"BH") |
sep |
character string used to separate the genes when concatenating |
Kai Guo
## Not run:
hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
gene=sample(unique(hsako$GeneID),1000)
res<-richLevel(gene,kodata = hsako,level="Level2")
## End(Not run)
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