parseAnnotation: parse an annotation file (a bidirectional map)

Description Usage Arguments

View source: R/clusterTools.R

Description

parses a bidirectional map of feature IDs vs. annotation terms, e.g. the GO annotation file at ftp://ftp.arabidopsis.org/home/tair/Ontologies/Gene_Ontology/ATH_GO_GOSLIM.txt.gz

Usage

1
parseAnnotation(got, idcol = 1, keycol = 6, termcol, rm.empty = TRUE)

Arguments

got

input table, e.g. a GO annotation

idcol

column where feature IDs can be found

keycol

column where annotation terms are found

termcol

optional column where a readable description of annotation terms is found; will only be used if keycol and termcol are a constant map, ie. each key is always associated with the same term; TODO: terminology?

rm.empty

rm all empty annotations; TODO: why does this occur?


raim/segmenTools documentation built on Nov. 9, 2018, 5:38 p.m.