Re: [Bioc-devel] VRanges-class positive strandness and locateVariants() strandawareness

[Robert Castelo]

Of course, the inclusion of strand would imply an interpretation of the 
variant and its strand (e.g., "-") with respect to an annotated feature. 
I can see a practical problem of integrity of the information on a 
VRanges object, by which a mandatory column, such as strand, depends on 
a non-mandatory column, such as some feature annotation stored as a 
metadata column.

A solution would be to add the transcript identifier (TXID) as mandatory 
column on the VRanges object but I suspect this is a big change to do, 
so adding a LOCSTRAND column (next to LOCSTART and LOCEND generated by 
locateVariants) in the metadata columns of the VRanges object would 
allow me to use a VRanges object as a container of variant x allele x 
sample x annotation.

Just to clear up the issue of merging strand and variant: a noisy 
variant (a variant that is not silent) and has a, e.g., loss-of-function 
effect such as the gain of a stop codon, is usually interpreted in the 
strand of the transcript and coding sequence in which the stop codon is 
gained, saying something like and A changed to a T producting the stop 
codon TAA. Ref and alt alleles are called in the strand of the reference 
chromosome, so if the transcript was annotated in the negative strand, 
we would know that we need to reverse-complement ref and alt to 
interpret the variant, although I see no need to do anything on the 
VRanges object to ref and alt because we know they are always in the 
strand of the reference chromosome. Only if you want to detect this 
stop-gain event (with predictCoding) then you would have to 
reverse-complement the ref and alt alleles. Conversely, if the variant 
falls in an intergenic region, then obviously the strand plays no role 
in the interpretation of the variant and nothing needs to be done when 
interpreting the ref and alt alleles.

On 6/11/15 5:47 PM, Michael Lawrence wrote:
The fact that the position describes the variant, but the strand
refers to the transcript is confusing to me. What is the concrete use
case for merging the two features like that? VRanges constrains its
strand for at least 2 reasons: (1) to be less error prone [of course
this runs completely counter to flexibility] and (2) simplicity [we
don't have to worry about what "-" means for ref/alt, overlap, etc].

On Thu, Jun 11, 2015 at 6:05 AM, Robert Castelo <robert.cast...@upf.edu> wrote:
one option for me is just to add a metadata column with the strand of the
overlapping feature. however, i'm interested to fully understand the
rationale behind this aspect of the design of the VRanges object.

a VRanges object unrolls variants in a VCF file per alternative allele and
sample. variants in VCF files are obtained from tallying reads aligned on a
reference genome. so, my understanding is that the reference allele is the
allele of the reference genome against which the reads were aligned while
the alternate allele(s) are allele calls different from the reference. from
this perspective, my interpretation is that ref and alt alleles have already
a strand, which is the strand of the reference chromosome against which the
reads were aligned to. i'm interested in this interpretation of the strand
of the variants because i'm interested in the interpretation of
sequence-features containing the reference and the alternate alleles, such
as differences in a binding site with the reference and the alternate
allele.

if we relax the meaning of elements in a VRanges object to, not only
variants x allele x sample, but to variants x allele x sample x
annotated-feature, then i think it would make sense to have the
strand-specific annotation in the strand slot of the VRanges object.

while this idea may be good or not for a number of reasons, i'm now mostly
interested in knowing whether i'm misinterpreting the design of VRanges
objects, and maybe variant calling in general or i'm in a more or less right
path in using a VRanges object to hold variant annotations.


thanks!!!

robert.


On 06/11/2015 04:30 AM, Michael Lawrence wrote:
I guess it depends on what the strand should mean. Would having a
negative strand indicate that the ref/alt should be complemented? I'm
not sure it's a good idea to conflate the strand of the variant itself
with the strand of an overlapping feature.

On Wed, Jun 10, 2015 at 1:17 PM, Robert Castelo<robert.cast...@upf.edu>
wrote:
my understanding was that VRanges is a container for variants and variant
annotations and strand is just one annotation more. when we use
locateVariants() a variant can be annotated to multiple transcripts where
in
one overlaps an exon, in another an intron and so on. In all those
transcripts annotations there is a strand annotation, the strand of the
transcript. if the transcript is annotated in the negative strand of the
reference chromosome then the annotation of a transcript region to a
variant
is going to be also on the negative strand.

both locateVariants() and predictCoding() return GRanges objects with
strand
annotations according to the transcripts being annotated. I thought it
made
sense in VariantFiltering to use VRanges objects as a  container for
variants and annotations and, for this reason, I would like to carry on
the
strand annotation into the VRanges object. Is there a strong reason for a
VRanges object, derived from GRanges, not to have strand?


On 6/10/15 6:26 PM, Michael Lawrence wrote:

VRanges is supposed to enforce strand. The goal is to use "*" always,
for simplicity and consistency with the result of readVcf(). Is there
a use case for negative strand variants?

On Wed, Jun 10, 2015 at 5:54 AM, Robert Castelo<robert.cast...@upf.edu>
wrote:

Michael,

regarding our email exchange three weeks ago, I found a couple of
places
in
VariantAnnotation that IMO need to be updated to avoid enforcing strand
on
VRanges.

these places occur when constructing and validating VRanges objects,
concretely at:

1. file R/methods-VRanges-class.R at the VRanges class constructor:

VRanges<-
     function(seqnames = Rle(), ranges = IRanges(),
              ref = character(), alt = NA_character_,
              totalDepth = NA_integer_, refDepth = NA_integer_,
              altDepth = NA_integer_, ..., sampleNames = NA_character_,
              softFilterMatrix = FilterMatrix(matrix(nrow = length(gr),
ncol =
0L),
                FilterRules()),
              hardFilters = FilterRules())
{
     gr<- GRanges(seqnames, ranges,
                   strand = .rleRecycleVector("*", length(ranges)), ...)
[...]

that precludes setting the strand at construction time:

library(VariantAnnotation)
VRanges(seqnames="chr1", ranges=IRanges(1, 5), ref="T", alt="C",
strand="-")
Error in GRanges(seqnames, ranges, strand = .rleRecycleVector("*",
length(ranges)),  :
     formal argument "strand" matched by multiple actual arguments


2. R/AllClasses.R at the VRanges class validity function
.valid.VRanges():

.valid.VRanges.strand<- function(object) {
     if (any(object@strand == "-"))
       paste("'strand' must always be '+' or '*'")
}

[...]

.valid.VRanges<- function(object)
{
     c(.valid.VRanges.ref(object),
       .valid.VRanges.alt(object),
       .valid.VRanges.strand(object),
       .valid.VRanges.depth(object))
}

that prompts an error when variants annotated on the negative strand
are
detected:

library(VariantAnnotation)
example(VRanges)
strand(vr)<- "-"
c(vr)
Error in validObject(.Object) :
     invalid class “VRanges” object: 'strand' must always be '+' or '*'


cheers,

robert.

On 05/22/2015 09:49 PM, Michael Lawrence wrote:

This changed recently. VariantAnnotation in devel no longer enforces a
strand on VRanges, or at least it allows the "*" case.


On Fri, May 22, 2015 at 11:33 AM, Robert
Castelo<robert.cast...@upf.edu
<mailto:robert.cast...@upf.edu>>  wrote:

       Hi,

       I have encountered myself in a strange situation when using the
       function locateVariants() from VariantAnnotation with an input
       VRanges object. The problem is that some of the expected coding
       annotations are not showing up when using locateVariants() with
       default parameters.

       After investigating this situation I think I found the reason,
which
       does not look like a bug but I would like that you give me some
       clarification about the logic behind using locateVariants() with
       VRanges objects.

       The documentation of the VRanges-class says that in this class
of
       objects "The strand is always constrained to be positive (+).".
I
       guess there may be a good reason for this but I could not find
it
in
       the documentation or googling about it.

       This means that when you coerce a CollapsedVCF object (obtained,
for
       example, from a VCF file via readVcf()) to a VRanges object,
even
       though variants in the VCF may have no strand, they get a
positive
       strand in the VRanges object.

       The problem arises then, when you call locateVariants() with
this
       VRanges object, because features on the negative strand are
never
       going to overlap with the variants since, by default, the
argument
       ignore.strand=FALSE.

       Let me illustrate this with a toy example. Consider the SNP
       rs1129038

(http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1129038)
at
       chr15:28356859 with allels A/G. It is located on the 3' UTR of
the
       gene HERC2 coded on the negative strand of the human reference
       genome. Let's build a toy VRanges object having this variant:

       library(VariantAnnotation)
       vr<- VRanges(seqnames="chr15",
                      ranges=IRanges(28356859, 28356859),
                      ref="A", alt="G",
                      refDepth=5, altDepth=7,
                      totalDepth=12, sampleNames="A")
       strand(vr)
       factor-Rle of length 1 with 1 run
          Lengths: 1
          Values : +
       Levels(3): + - *

       Let's build now its CollapsedVCF counterpart by using the
       corresponding coercion method and set the strand to "*":

       vcf<- asVCF(vr)
       strand(vcf)<- "*"

       Now run locateVariants() on both objects with UCSC annotations:

       library(TxDb.Hsapiens.UCSC.hg19.knownGene)
       txdb<- TxDb.Hsapiens.UCSC.hg19.knownGene

       locateVariants(vcf, txdb, region=AllVariants())
       GRanges object with 2 ranges and 9 metadata columns:
              seqnames               ranges strand | LOCATION  LOCSTART
       LOCEND   QUERYID        TXID         CDSID
       <Rle>  <IRanges>  <Rle>  |<factor>  <integer>  <integer>
<integer>
       <character>  <IntegerList>
          [1]    chr15 [28356859, 28356859]      * | threeUTR        50
50
               1       55386
          [2]    chr15 [28356859, 28356859]      * | threeUTR        50
50
               1       55387
                   GENEID       PRECEDEID        FOLLOWID
       <character>  <CharacterList>  <CharacterList>
          [1]        8924
          [2]        8924
          -------
          seqinfo: 1 sequence from an unspecified genome; no seqlengths

       locateVariants(vr, txdb, region=AllVariants())
       GRanges object with 1 range and 9 metadata columns:
              seqnames               ranges strand |   LOCATION
LOCSTART
       LOCEND   QUERYID      TXID         CDSID
       <Rle>  <IRanges>  <Rle>  |<factor>  <integer>  <integer>
<integer>
       <integer>  <IntegerList>
          [1]    chr15 [28356859, 28356859]      + | intergenic<NA>
<NA>
               1<NA>
                   GENEID                         PRECEDEID
FOLLOWID
       <character>  <CharacterList>  <CharacterList>
          [1]<NA>  100132565,100289656,100616223,...            2567
          -------
          seqinfo: 1 sequence from an unspecified genome; no seqlengths

       Note that while we get the 3' UTR annotation from the strandless
VCF
       object we do not get it from the VRanges object with the
positive
       strand. To make my point clear: this positive strand shows up
when
       you coerce a strandless VCF object to a VRanges one, because
       positive strandness seems to be the convention for VRanges
objects:

       as(vcf, VRanges)
       VRanges object with 1 range and 1 metadata column:
              seqnames               ranges strand         ref
       alt     totalDepth       refDepth       altDepth
       <Rle>  <IRanges>  <Rle>  <character>  <characterOrRle>
<integerOrRle>
       <integerOrRle>  <integerOrRle>
          [1]    chr15 [28356859, 28356859]      +           A
          G             12              5              7
                sampleNames softFilterMatrix |      QUAL
       <factorOrRle>  <matrix>  |<numeric>
          [1]             A                  |<NA>
          -------
          seqinfo: 1 sequence from an unspecified genome; no seqlengths
          hardFilters: NULL


       Of course, if I run locateVariants() with the argument
       ignore.strand=TRUE, then I get the expected annotation:

       locateVariants(vr, txdb, region=AllVariants(),
ignore.strand=TRUE)
       GRanges object with 2 ranges and 9 metadata columns:
              seqnames               ranges strand | LOCATION  LOCSTART
       LOCEND   QUERYID        TXID         CDSID
       <Rle>  <IRanges>  <Rle>  |<factor>  <integer>  <integer>
<integer>
       <character>  <IntegerList>
          [1]    chr15 [28356859, 28356859]      + | threeUTR       677
       677         1       55386
          [2]    chr15 [28356859, 28356859]      + | threeUTR       677
       677         1       55387
                   GENEID       PRECEDEID        FOLLOWID
       <character>  <CharacterList>  <CharacterList>
          [1]        8924
          [2]        8924
          -------
          seqinfo: 1 sequence from an unspecified genome; no seqlengths


       So, my question is, given that VRanges objects are enforced to
have
       a positive strand, would not be better to have
ignore.strand=TRUE
as
       default in locateVariants?

       Alternatively, I would recommend that locateVariants() issues a
       warning, or maybe an error, when the input object is VRanges and
       ignore.strand=FALSE.

       Finally, out of curiosity, why a VRanges object enforces the
       positive strand in all its genomic ranges? Would not be better
just
       taking the strand of the CollapsedVCF object when coercing the
       CollapsedVCF object to VRanges?


       thanks!!


       robert.

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--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550

_______________________________________________
Bioc-devel@r-project.org mailing list
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--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550

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Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel