addGoAnnotations {pRoloc} | R Documentation

## Add GO annotations

### Description

Adds GO annotations to the feature data

### Usage

    addGoAnnotations(object, params, evidence, useID = FALSE,
      fcol = "GOAnnotations", ...)

### Arguments

`object` | An instance of class `MSnSet`.
`params` | An instance of class `AnnotationParams`. If missing, `getAnnotationParams` will be used.
`evidence` | GO evidence filtering.
`useID` | Logical. Should GO term names or identifiers be used? If `TRUE`, identifiers will be used. If `FALSE` GO term names will be used.
`fcol` | Character. Name of the matrix of annotations to be added to the `fData` default is `GOAnnotations`
`...` | Other arguments passed to `makeGoSet`

### Value

An updated `MSnSet` with new feature data column called `GOAnnotations` containing a matrix of GO annotations

### Author(s)

Lisa M Breckels

### Examples

    library(pRolocdata)
    data(dunkley2006)
    par <- setAnnotationParams(inputs =
                       c("Arabidopsis thaliana genes",
                       "Gene stable ID"))
    ## add protein sets/annotation information
    xx <- addGoAnnotations(dunkley2006, par)
    dim(fData(xx)$GOAnnotations)

    ## filter sets
    xx <- filterMinMarkers(xx, n = 50)
    dim(fData(xx)$GOAnnotations)
    xx <- filterMaxMarkers(xx, p = .25)
    dim(fData(xx)$GOAnnotations)

    ## Subset for specific protein sets
    sub <- subsetMarkers(xx, keep = c("vacuole"))

    ## Order protein sets
    res <- orderGoAnnotations(xx, k = 1:3, p = 1/3, verbose = FALSE)
    if (interactive()) {
    pRolocVis(res, fcol = "GOAnnotations")
    }

[Package pRoloc version 1.22.2 Index]