addGoAnnotations: Add GO annotations

Description Usage Arguments Value Author(s) Examples

Description

Adds GO annotations to the feature data

Usage

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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

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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")
}


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