getEnrichmentTable: Convert uniprot download to table protein entry and go column

In protViz/topGOUniProt: GO annotation for uniprot

Description

Convert uniprot download to table protein entry and go column

Usage

getEnrichmentTable(enrich, background, mapping, topNodes = 15,
  ontology = "BP")

Arguments

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

Examples

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

protViz/topGOUniProt documentation built on May 26, 2019, 10:31 a.m.