addGoAnnotations: Add GO annotations

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

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")
}

lgatto/pRoloc documentation built on Nov. 27, 2024, 12:14 a.m.