Add GO annotations

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

Lisa M Breckels

Examples

library(pRolocdata)
data(dunkley2006)
par <- setAnnotationParams(inputs =
                   c("Arabidopsis thaliana genes",
                   "Gene stable ID"))
#> Using species Arabidopsis thaliana genes (TAIR10)
#> Warning: Ensembl will soon enforce the use of https.
#> Ensure the 'host' argument includes "https://"
#> Using feature type Gene stable ID(s) [e.g. AT1G01010]
#> Connecting to Biomart...
#> Warning: Ensembl will soon enforce the use of https.
#> Ensure the 'host' argument includes "https://"
## add protein sets/annotation information
xx <- addGoAnnotations(dunkley2006, par)
dim(fData(xx)$GOAnnotations)
#> [1] 689  79

## filter sets
xx <- filterMinMarkers(xx, n = 50)
#> Retaining 3 out of 79 in GOAnnotations
dim(fData(xx)$GOAnnotations)
#> [1] 689   3
xx <- filterMaxMarkers(xx, p = .25)
#> Retaining 2 out of 3 in GOAnnotations
dim(fData(xx)$GOAnnotations)
#> [1] 689   2

## Subset for specific protein sets
sub <- subsetMarkers(xx, keep = c("vacuole"))
#> Warning: GO markers vacuole not found

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