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
The resulting object is a data frame containing the terms of
slimCollection as row labels, counts and frequencies of
identifiers classified to each term, and an abbreviated term
An identifier in
idSrc can expand to several 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
goSlim(idSrc, slimCollection, ontology, ..., verbose=FALSE)
An argument determining the source of GO terms to be
mapped to slim terms. The source might be a
An argument containing the GO slim terms.
A character string naming the ontology to be consulted when identifying slim term hierarchies. One of ‘MF’ (molecular function), ‘BP’ (biological process), ‘CC’ (cellular compartment).
Additional arguments passed to specific methods.
Logical influencing whether messages (primarily missing GO terms arising during creation of the slim hierarchy) are reported.
slimCollection categories. The hierarchy of
terms included for each term is from the ontology (MF, BP, or CC)
verbose informs about, e.g., GO
terms that are not found.
Determine the (unique) GO terms
implied by feature names in
idSrc (using the annotation map
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")
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