Message-ID: <52EFC9B8.4050808@embl.de>
Date: 2014-02-03T16:54:16Z
From: Julian Gehring
Subject: [Bioc-devel] ggbio: Support of object inheriting from 'GRanges'
Hi,
while ggbio work well for 'GRanges' objects, it is not able to deal with
objects inheriting from a 'GRanges', e.g. a 'VRanges' object:
library(ggbio)
library(GenomicRanges)
library(VariantAnnotation)
gr = GRanges("1", IRanges(1, 10))
vr = as(gr, "VRanges")
autoplot(gr) ## works
autoplot(vr) ## breaks
The simple workaround would be to convert back to a 'GRanges' first by
hand. But shouldn't ggbio be able to handle these cases? Is this
related to the different defaults of strands between GRanges and VRanges?
Best wishes
Julian