getGOFromFeatures: Retrieve GO terms for feature names

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

Retrieve GO terms for feature names

Description

The function pulls the gene ontology (GO) terms for a set of feature names.

Usage

getGOFromFeatures(
  id,
  namespace = "cellular_component",
  evidence = NULL,
  params = NULL,
  verbose = FALSE,
  nmax = 500
)

Arguments

id	An character with feature names to be pulled from biomart. If and MSnSet is provided, then featureNames(id) is used.
namespace	The GO namespace. One of biological_process, cellular_component (default) or molecular_function.
evidence	The GO evidence code. See showGOEvidenceCodes for details. If NULL (default), no filtering based on the evidence code is performed.
params	An instance of class "AnnotationParams".
verbose	A logical defining verbosity of the function. Default is FALSE.
nmax	As described in https://support.bioconductor.org/p/86358/, the Biomart result can be unreliable for large queries. This argument splits the input in chunks of length nmax (default is 500). If set to NULL, the query is performed in full.

Value

A data.frame with relevant GO terms.

Author(s)

Laurent Gatto

Examples

library(pRolocdata)
data(dunkley2006)
data(dunkley2006params)
dunkley2006params
fn <- featureNames(dunkley2006)[1:5]
getGOFromFeatures(fn, params = dunkley2006params)

lgatto/pRoloc documentation built on Oct. 23, 2024, 12:51 a.m.