parseAnnotation: Parse an annotation file (a bidirectional map)

In raim/segmenTools: Tools for Functional Genome Exploration

Parse an annotation file (a bidirectional map)

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 and returns a TRUE/FALSE table that can be used as input to clusterAnnotation.

Usage

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 April 25, 2024, 10:14 a.m.