Description Usage Arguments Value Examples
This function is to do GSEA enrichment analysis
1 2 | Fun.enrich_withFC(markergenesList, All.genes = all.genes.refer,
db = msig.db, qcutoff = 0.05, top = NULL)
|
markergenesList |
is a list containing several elements each of which is a vector of gene names |
All.genes |
the background genes data(all.genes.refer) |
db |
=msig.db the term database to use, default is the msig.db; data(msig.db) |
qcutoff=0.05 |
the term to show with q value lower than 0.05 |
top=NULL |
pass a number to only show top # terms |
this will return a simple object with two elements, one is the table to show the significant terms , the other one shows the gene names involved significant terms
1 | S7G.GSEA<-Fun.enrich_withFC(markergenesList=list(S7G=topS7G.genes),All.genes=all.genes.refer)
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