goSlim-methods {GSEABase} | R Documentation |
These methods summarize the gene ontology terms implied by the
idSrc
argument into the GO terms implied by the
slimCollection
argument. The summary takes identifiers in
idSrc
and determines all GO terms that
apply to the identifiers. This full list of GO terms are then
classified for membership in each term in the
slimCollection
.
The resulting object is a data frame containing the terms of
slimCollection
as row labels, counts and frequencies of
identifiers calssified to each term, and an abbreviated term
description.
An identifier in idSrc
can expand to serveral GO terms, and the
GO terms in slimCollection
can imply an overlapping hierarchy
of terms. Thus the resulting summary can easily contain more counts
than there are identifiers in idSrc
.
goSlim(idSrc, slimCollection, ontology, ..., verbose=FALSE)
idSrc |
An argument determining the source of GO terms to be
mapped to slim terms. The source might be a GOCollection of
terms, or another object (e.g., ExpressionSet) for which the method
can extract GO terms. |
slimCollection |
An argument containing the GO slim terms. |
ontology |
A character string nameing the ontology to be consulted when identifing slim term hierarchies. One of ‘MF’ (molecular function), ‘BP’ (biological process), ‘CC’ (cellular compartment). |
... |
Additional arguments passed to specific emthods. |
verbose |
Logical influencing whether messages (primarily missing GO terms arising during creation of the slim hierarchy) are reported. |
idSrc
GO
terms into slimCollection
categories. The hierarchy of
terms included for each term is from the ontology (MF, BP, or CC)
specified by ontology
. verbose
informs about, e.g., GO
terms that are not found.idSrc
(using the annotation map
identified in annotation(idSrc)
).myIds <- c("GO:0016564", "GO:0003677", "GO:0004345", "GO:0008265", "GO:0003841", "GO:0030151", "GO:0006355", "GO:0009664", "GO:0006412", "GO:0015979", "GO:0006457", "GO:0005618", "GO:0005622", "GO:0005840", "GO:0015935", "GO:0000311") myCollection <- GOCollection(myIds) fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase") slim <- getOBOCollection(fl) goSlim(myCollection, slim, "MF") data(sample.ExpressionSet) goSlim(sample.ExpressionSet, slim, "MF", evidenceCode="TAS")