richGSEA,ANY,data.frame-method | R Documentation |
GSEA Enrichment analysis function
## S4 method for signature 'ANY,data.frame'
richGSEA(
x,
object,
keytype = "",
pvalue = 0.05,
padj = NULL,
minSize = 15,
ontology = ontology,
maxSize = 500,
padj.method = "BH",
organism = NULL,
table = TRUE,
sep = ","
)
x |
a vector include all log2FC with gene name |
object |
annotation file for all genes |
pvalue |
pvalue cutoff value |
padj |
adjust p value cut off method |
minSize |
Minimal size of a gene set to test. All pathways below the threshold are excluded. |
maxSize |
Maximal size of a gene set to test. All pathways above the threshold are excluded. |
padj.method |
p value adjust method |
table |
leadingEdge as vector |
sep |
character string used to separate the genes when concatenating |
Kai Guo
## Not run:
hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
hsako<-as.data.frame(hsako)
name=sample(unique(hsako$GeneID),1000)
gene<-rnorm(1000)
names(gene)<-name
res<-richGSEA(gene,object = hsako)
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.