Adds GO annotations to the feature data
addGoAnnotations(
object,
params,
evidence,
useID = FALSE,
fcol = "GOAnnotations",
...
)
An instance of class MSnSet
.
An instance of class AnnotationParams
.
If missing, getAnnotationParams
will be used.
GO evidence filtering.
Logical. Should GO term names or identifiers be used?
If TRUE
, identifiers will be used. If FALSE
GO term
names will be used.
Character. Name of the matrix of annotations to be added to the
fData
default is GOAnnotations
Other arguments passed to makeGoSet
An updated MSnSet
with new feature data column
called GOAnnotations
containing a matrix of GO
annotations
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)$GOAnnotations)
#> [1] 689 165
## filter sets
xx <- filterMinMarkers(xx, n = 50)
#> Retaining 18 out of 165 in GOAnnotations
dim(fData(xx)$GOAnnotations)
#> [1] 689 18
xx <- filterMaxMarkers(xx, p = .25)
#> Retaining 14 out of 18 in GOAnnotations
dim(fData(xx)$GOAnnotations)
#> [1] 689 14
## 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)
#> Calculating GO cluster densities
if (interactive()) {
pRolocVis(res, fcol = "GOAnnotations")
}