goSlim-methods {GSEABase} | R Documentation

## Methods for Function goSlim in Package ‘GSEABase’

### Description

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 classified to each term, and an abbreviated term description.

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 `idSrc`.

### Usage

    goSlim(idSrc, slimCollection, ontology, ..., verbose=FALSE)

### Arguments

`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 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.
`verbose` | Logical influencing whether messages (primarily missing GO terms arising during creation of the slim hierarchy) are reported.

### Methods

idSrc="GOCollection", slimCollection="GOCollection", ontology="character", ..., verbose=FALSE

  Classify `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="ExpressionSet", slimCollection="GOCollection", ontology="character", ..., verbose=FALSE

  Determine the (unique) GO terms implied by feature names in `idSrc` (using the annotation map identified in `annotation(idSrc)`).

### Examples

    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")

[Package GSEABase version 1.54.0 Index]