library(pRolocdata)
data(dunkley2006)
par <- setAnnotationParams(inputs =
c("Arabidopsis thaliana genes",
"TAIR locus 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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