Re: [Bioc-devel] restrictToSNV for VCF
Update on these tasks.
1) XStringSetList now has an nchar() method (as of Biostrings 2.31.17)
2) restrictToSNV() was removed from VariantAnnotation
3) The following generics and methods for VCF and VRanges have been
added to VariantAnnotation 1.9.50:
isSNV()
isInsertion()
isDeletion()
isIndel()
isSubstitution
isTranstion()
I've held off on adding
isSV()
isSVPrecise()
until we have a way to distinguish structural vs non-structual ALT.
Currently if any of the ALT values are structural, all are coerced to
character. It would be good to have a way to distinguish a mixture of
ALT values so we can compute on the nucleotides and do whatever else on
the structural variants. This may be a project for the next dev cycle.
Valerie
On 03/19/2014 03:29 PM, Michael Lawrence wrote:
Thanks Sean. Probably also need an isSubstitution for any
substitution, either SNV or complex.
On Wed, Mar 19, 2014 at 3:20 PM, Sean Davis sdav...@mail.nih.gov
mailto:sdav...@mail.nih.gov wrote:
On Wed, Mar 19, 2014 at 4:26 PM, Valerie Obenchain
voben...@fhcrc.org mailto:voben...@fhcrc.org wrote:
Thanks for the feedback.
I'll look into nchar for XStringSetList.
I'm in favor of supporting isDeletion(), isInsertion(),
isIndel() and isSNV() for the VCF classes and removing
restrictToSNV(). I could add an argument 'all_alt' or
'all_alt_agreement' to be used with CollapsedVCF in the case
where not all alternate alleles meet the criteria.
Here are the current definitions:
isDeletion - function(x) {
nchar(alt(x)) == 1L nchar(ref(x)) 1L
substring(ref(x), 1, 1) == alt(x)
}
isInsertion - function(x) {
nchar(ref(x)) == 1L nchar(alt(x)) 1L
substring(alt(x), 1, 1) == ref(x)
}
isIndel - function(x) {
isDeletion(x) | isInsertion(x)
}
isSNV - function(x) {
nchar(alt(x)) == 1L nchar(ref(x)) == 1L
}
To be thorough:
isTransition()
isSV()
isSVPrecise()
We haven't been using VCF for SVs much yet, but there are probably
some fun things to be done on that front.
Sean
Valerie
On 03/19/2014 01:07 PM, Vincent Carey wrote:
On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence
lawrence.mich...@gene.com
mailto:lawrence.mich...@gene.com
mailto:lawrence.michael@gene.__com
mailto: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 mailto:voben...@fhcrc.org
mailto:voben...@fhcrc.org mailto: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
Re: [Bioc-devel] restrictToSNV for VCF
Hi Martin, On 03/21/2014 01:45 PM, Martin Morgan wrote: On 03/20/2014 05:20 PM, Hervé Pagès wrote: 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 I think of a SummarizedExperiment as fundamentally a matrix with row and column annotations. 'length' would then be prod(dim(se1)) But it's not defined as such either. Note that findOverlaps() on SummarizedExperiment objects returns a Hits object with indices in the 1:nrow(query) or 1:nrow(subject) range. I'd like to be able to say in the seq_along(query) or seq_along(subject) range because that's what findOverlaps() does on any other object defined in IRanges/GenomicRanges/GenomicAlignments. But I can't because that would be inaccurate. However, it's conceptually true: I can use the indices in the Hits object to do 1D extractions from the query or subject. This is good and consistent with any other type of query or subject. col- and rownames() are defined but names() is NULL. I guess 1-D sub-setting isn't matrix-like, but I don't think that removing this 'feature' simply for consistency sake is worth it; I was not suggesting that. I guess the subsetting logical was copy/pasted from other code without enough thought. head(), tail() could be implemented if this were somehow useful (I usually use these for compact display, and that's irrelevant here...); I still find it sometimes useful to be able to do head() on a big object when I just want to try things on a few elements first: dim(vcf) [1] 100 3 toy - head(vcf) rowData(toy) assay(toy) isSNV(toy) findOverlaps(toy, exons) It's more convenient and much quicker than having to truncate the individual results: head(rowData(vcf)) head(assay(vcf)) head(isSNV(vcf)) head(findOverlaps(vcf, exons)) I guess what I'm trying to say is that while it helps thinking of a SummarizedExperiment as fundamentally a matrix, there are already enough differences with the matrix API to suggest that, unlike for a matrix, the length of a SummarizedExperiment object is its nb of rows. It's implicit in many ways and I think that formalizing it would help rather than hurt. It will still be somewhat a surprise for the end-user, but not a bigger surprise than the ones s/he gets right now with seq_along(vcf), vcf[i], isSNV(vcf), findOverlaps(), head(), etc.. And once s/he gets over it, there won't be anymore surprises: all these things will be in agreement with length(vcf) and behave as expected. Thanks, H. rev() on a matrix doesn't do anything useful. Martin 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.eduwrote: 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.orgwrote: Hi, I've added a restrictToSNV() function to
Re: [Bioc-devel] restrictToSNV for VCF
Some of the inconsistency emerges from wrappers that correspond to operations on the rowData. I think that's fine as long as it's obvious (as in the case of findOverlaps and isSNV). The head and tail functions are by convention row-based for rectangular objects. I agree though that if we keep 1D extraction then the behavior of length() should be changed. On Fri, Mar 21, 2014 at 3:35 PM, Hervé Pagès hpa...@fhcrc.org wrote: Hi Martin, On 03/21/2014 01:45 PM, Martin Morgan wrote: On 03/20/2014 05:20 PM, Hervé Pagès wrote: 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 I think of a SummarizedExperiment as fundamentally a matrix with row and column annotations. 'length' would then be prod(dim(se1)) But it's not defined as such either. Note that findOverlaps() on SummarizedExperiment objects returns a Hits object with indices in the 1:nrow(query) or 1:nrow(subject) range. I'd like to be able to say in the seq_along(query) or seq_along(subject) range because that's what findOverlaps() does on any other object defined in IRanges/GenomicRanges/GenomicAlignments. But I can't because that would be inaccurate. However, it's conceptually true: I can use the indices in the Hits object to do 1D extractions from the query or subject. This is good and consistent with any other type of query or subject. col- and rownames() are defined but names() is NULL. I guess 1-D sub-setting isn't matrix-like, but I don't think that removing this 'feature' simply for consistency sake is worth it; I was not suggesting that. I guess the subsetting logical was copy/pasted from other code without enough thought. head(), tail() could be implemented if this were somehow useful (I usually use these for compact display, and that's irrelevant here...); I still find it sometimes useful to be able to do head() on a big object when I just want to try things on a few elements first: dim(vcf) [1] 100 3 toy - head(vcf) rowData(toy) assay(toy) isSNV(toy) findOverlaps(toy, exons) It's more convenient and much quicker than having to truncate the individual results: head(rowData(vcf)) head(assay(vcf)) head(isSNV(vcf)) head(findOverlaps(vcf, exons)) I guess what I'm trying to say is that while it helps thinking of a SummarizedExperiment as fundamentally a matrix, there are already enough differences with the matrix API to suggest that, unlike for a matrix, the length of a SummarizedExperiment object is its nb of rows. It's implicit in many ways and I think that formalizing it would help rather than hurt. It will still be somewhat a surprise for the end-user, but not a bigger surprise than the ones s/he gets right now with seq_along(vcf), vcf[i], isSNV(vcf), findOverlaps(), head(), etc.. And once s/he gets over it, there won't be anymore surprises: all these things will be in agreement with length(vcf) and behave as expected. Thanks, H. rev() on a matrix doesn't do anything useful. Martin 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.eduwrote: 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
Re: [Bioc-devel] restrictToSNV for VCF
On 03/20/2014 05:20 PM, Hervé Pagès wrote: [...] Following that logic names(se1) also probably return colnames(se1). /\ should H. H. On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey st...@channing.harvard.eduwrote: 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.orgwrote: 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 REFALT DNAStringSet DNAStringSetList 1 G A 2 AA TT 3 TG,A 4 G TT,C Thanks. Valerie ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] restrictToSNV for VCF
Also, the code for DNAStringSetList is too low-level. There should just be an nchar,XStringSetList that does the same thing as nchar,CompressedCharacterList. Then restrictToSNV or whatever just does any(nchar(x) == 1L) for any List. Michael On Wed, Mar 19, 2014 at 1:00 PM, Michael Lawrence micha...@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? Michael On Tue, Mar 18, 2014 at 10:36 AM, Valerie Obenchain voben...@fhcrc.orgwrote: 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 REFALT DNAStringSet DNAStringSetList 1 G A 2 AA TT 3 TG,A 4 G TT,C Thanks. Valerie ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] restrictToSNV for VCF
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.orgwrote: 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 REFALT DNAStringSet DNAStringSetList 1 G A 2 AA TT 3 TG,A 4 G TT,C Thanks. Valerie ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] restrictToSNV for VCF
You can apparently use 1D extraction for VCF, which is a little surprising; I learned it from restrictToSNV. On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey st...@channing.harvard.eduwrote: 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.orgwrote: 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 REFALT DNAStringSet DNAStringSetList 1 G A 2 AA TT 3 TG,A 4 G TT,C Thanks. Valerie ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] restrictToSNV for VCF
Thanks Sean. Probably also need an isSubstitution for any substitution,
either SNV or complex.
On Wed, Mar 19, 2014 at 3:20 PM, Sean Davis sdav...@mail.nih.gov wrote:
On Wed, Mar 19, 2014 at 4:26 PM, Valerie Obenchain voben...@fhcrc.orgwrote:
Thanks for the feedback.
I'll look into nchar for XStringSetList.
I'm in favor of supporting isDeletion(), isInsertion(), isIndel() and
isSNV() for the VCF classes and removing restrictToSNV(). I could add an
argument 'all_alt' or 'all_alt_agreement' to be used with CollapsedVCF in
the case where not all alternate alleles meet the criteria.
Here are the current definitions:
isDeletion - function(x) {
nchar(alt(x)) == 1L nchar(ref(x)) 1L substring(ref(x), 1, 1) ==
alt(x)
}
isInsertion - function(x) {
nchar(ref(x)) == 1L nchar(alt(x)) 1L substring(alt(x), 1, 1) ==
ref(x)
}
isIndel - function(x) {
isDeletion(x) | isInsertion(x)
}
isSNV - function(x) {
nchar(alt(x)) == 1L nchar(ref(x)) == 1L
}
To be thorough:
isTransition()
isSV()
isSVPrecise()
We haven't been using VCF for SVs much yet, but there are probably some
fun things to be done on that front.
Sean
Valerie
On 03/19/2014 01:07 PM, Vincent Carey wrote:
On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence
lawrence.mich...@gene.com mailto: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 mailto: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
REFALT
DNAStringSet DNAStringSetList
1 G A
2 AA TT
3 TG,A
4 G TT,C
Thanks.
Valerie
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--
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: voben...@fhcrc.org
Phone: (206) 667-3158
Fax:(206) 667-1319
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