Description Usage Arguments Examples
Convert uniprot download to table protein entry and go column
1 2 | getEnrichmentTable(enrich, background, mapping, topNodes = 15,
ontology = "BP")
|
enrich |
list of proteins |
background |
background proteins |
mapping |
default getHumanData() or getMouseData() |
topNodes |
nr top categories |
ontology |
ontology to use i.e. BB or CC |
1 2 3 4 5 6 7 8 9 10 11 12 13 | library(topGOUniProt)
tmp <- uniprotTable2ProteinGOTable(mapping=getMouseData(), ontology="GO")
head(tmp)
pids <- unique(tmp[,"Entry"] )
res <- getEnrichmentTable(pids[1:100], pids[1:1000] , mapping = getMouseData(0), topNodes = 15, ontology = "BP")
res
tmp <- uniprotTable2ProteinGOTable(mapping=getHumanData(),ontology="GO")
head(tmp)
pids <- unique(tmp[,"Entry"] )
res <- getEnrichmentTable(pids[1:2000], pids ,mapping = getMouseData(0), topNodes = 15, ontology = "MF")
res
res <- getEnrichmentTable(pids[1:2000], pids , getMouseData(0), topNodes = 15, ontology = "CC")
res
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