addGoAnnotations {pRoloc} | R Documentation |
Adds GO annotations to the feature data
addGoAnnotations(object, params, evidence, useID = FALSE, fcol = "GOAnnotations", ...)
object |
An instance of class |
params |
An instance of class |
evidence |
GO evidence filtering. |
useID |
Logical. Should GO term names or identifiers be used?
If |
fcol |
Character. Name of the matrix of annotations to be added to the
|
... |
Other arguments passed to |
An updated MSnSet
with new feature data column
called GOAnnotations
containing a matrix of GO
annotations
Lisa M Breckels
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") }