Hi,
Assume that we have two variants from two samples at the same locus,
stored in a 'VRanges' or 'VCF' object:
library(VariantAnnotation)
vr = VRanges("1", IRanges(c(10, 10), width = 1),
ref = c("C", "C"), alt = c("A", "G"),
sampleNames = c("S1", "S2"))
vcf = as(vr, "VCF")
If we
The two data structures do not encode the same information. Coercion to VCF
forms a rectangular matrix: position+alt by sample. There is no standard
way to encode that a given cell in that matrix is absent, so coercion to
VRanges simply maps each cell to an element. One could imagine using the
"."
I don't see how this can be fixed. The two data structures are semantically
incompatible; they encode different types of information, so information is
lost in both directions. Even if we collapsed the alts, there is no way (as
far as I know) to say that data for one individual + alt combination is
(Resending - the last message didn't post to the list.)
I was thinking the absence of a header in VRanges would make collapsing
difficult and with your comments it's clear this isn't a good idea.
I like the description you gave of the differences in class content and
geometry and have added t
