Hi,
On 03/19/2014 01:10 PM, Michael Lawrence wrote:
You can apparently use 1D extraction for VCF, which is a little surprising;
I learned it from restrictToSNV.
This is inherited from SummarizedExperiment:
> example(SummarizedExperiment)
> se1
class: SummarizedExperiment
dim: 200 6
exptData(0):
assays(1): counts
rownames: NULL
rowData metadata column names(0):
colnames(6): A B ... E F
colData names(1): Treatment
> se1[1:4]
class: SummarizedExperiment
dim: 4 6
exptData(0):
assays(1): counts
rownames: NULL
rowData metadata column names(0):
colnames(6): A B ... E F
colData names(1): Treatment
To me that means that a SummarizedExperiment has a length
(conceptually), and that this length is the number of rows.
It would actually help if a "length" method was defined:
> length(se1)
[1] 1
That would automatically fix many convenience [ wrappers like head(),
tail(), rev(), etc...
> head(se1)
class: SummarizedExperiment
dim: 1 6
exptData(0):
assays(1): counts
rownames: NULL
rowData metadata column names(0):
colnames(6): A B ... E F
colData names(1): Treatment
> rev(se1)
class: SummarizedExperiment
dim: 1 6
exptData(0):
assays(1): counts
rownames: NULL
rowData metadata column names(0):
colnames(6): A B ... E F
colData names(1): Treatment
Following that logic names(se1) also probably return colnames(se1).
H.
On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey
<st...@channing.harvard.edu>wrote:
On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence <
lawrence.mich...@gene.com> wrote:
It would be nice to have functions like isSNV, isIndel, isDeletion, etc
that at least provide precise definitions of the terminology. I've added
these, but they're designed only for VRanges. Should work for ExpandedVCF.
Also, it would be nice if restrictToSNV just assumed that alt(x) must be
something with nchar() support (with special handling for any List), so
that the 'character' vector of alt,VRanges would work immediately.
Basically restrictToSNV should just be x[isSNV(x)]. Is there even a
use-case for the restrictToSNV abstraction if we did that?
for VCF instance it would be x[isSNV(x),] and indeed I think that would be
sufficient. i like the idea of having this family of predicates for
variant classes to allow such selections
Michael
On Tue, Mar 18, 2014 at 10:36 AM, Valerie Obenchain <voben...@fhcrc.org>wrote:
Hi,
I've added a restrictToSNV() function to VariantAnnotation (1.9.46). The
return value is a subset VCF object containing SNVs only. The function
operates on CollapsedVCF or ExapandedVCF and the alt(VCF) value must be
nucleotides (i.e., no structural variants).
A variant is considered a SNV if the nucleotide sequences in both
ref(vcf) and alt(x) are of length 1. I have a question about how variants
with multiple 'ALT' values should be handled.
Should we consider row 4 a SNV? One 'ALT' is length 1, the other is not.
ALT <- DNAStringSetList("A", c("TT"), c("G", "A"), c("TT", "C"))
REF <- DNAStringSet(c("G", c("AA"), "T", "G"))
DataFrame(REF, ALT)
DataFrame with 4 rows and 2 columns
REF ALT
<DNAStringSet> <DNAStringSetList>
1 G A
2 AA TT
3 T G,A
4 G TT,C
Thanks.
Valerie
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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