getGOFromFeatures {pRoloc} | R Documentation

## 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)

[Package pRoloc version 1.22.2 Index]