locateVariants {VariantAnnotation} | R Documentation

## Locate variants

### Description

Variant location with respect to gene function

### Usage

    locateVariants(query, subject, region, ...)
    ## S4 method for signature 'VCF,TxDb,VariantType'
    locateVariants(query, subject, region, ...,
        cache=new.env(parent=emptyenv()), ignore.strand=FALSE, asHits=FALSE)
    ## S4 method for signature 'GRanges,TxDb,VariantType'
    locateVariants(query, subject, region, ...,
        cache=new.env(parent=emptyenv()), ignore.strand=FALSE, asHits=FALSE)

### Arguments

`query` | A IntegerRanges, GRanges or VCF object containing the variants. Metadata columns are allowed but ignored. NOTE: Zero-width ranges are treated as width-1 ranges; start values are decremented to equal the end value.
`subject` | A TxDb or `GRangesList` object that serves as the annotation. GFF files can be converted to TxDb objects with `makeTxDbFromGFF()` in the `GenomicFeatures` package.
`region` | An instance of one of the 8 VariantType classes: `CodingVariants`, `IntronVariants`, `FiveUTRVariants`, `ThreeUTRVariants`, `IntergenicVariants`, `SpliceSiteVariants`, `PromoterVariants`, `AllVariants`. All objects can be instantiated with no arguments, e.g., CodingVariants() will create an object of `CodingVariants`. `AllVariants`, `PromoterVariants` and `IntergenicVariants` have `upstream` and `downstream` arguments. For `PromoterVariants` and `IntergenicVariants` these are single integer values >= 0. For `AllVariants` these are integer vectors of length 2 named ‘promoter’ and ‘intergenic’. See ?`upstream` for more details. When using `AllVariants`, a range in `query` may fall in multiple regions (e.g., 'intergenic' and 'promoter'). In this case the result will have a row for each match. All data in the row will be equivalent except the LOCATION column.
`...` | Additional arguments passed to methods
`cache` | An `environment` into which required components of `subject` are loaded. Provide, and re-use, a cache to speed repeated queries to the same `subject` across different `query` instances.
`ignore.strand` | A `logical` indicating if strand should be ignored when performing overlaps.
`asHits` | A `logical` indicating if the results should be returned as a Hits object. Not applicable when `region` is AllVariants or IntergenicVariants.

### Details

Range representation:

  The ranges in `query` should reflect the position(s) of the reference allele. For snps the range will be of width 1. For range insertions or deletions the reference allele could be a sequence such as GGTG in which case the width of the range should be 4.

Location:

  Possible locations are ‘coding’, ‘intron’, ‘threeUTR’, ‘fiveUTR’, ‘intergenic’, ‘spliceSite’, or ‘promoter’.

  Overlap operations for ‘coding’, ‘intron’, ‘threeUTR’, and ‘fiveUTR’ require variants to fall completely within the defined region to be classified as such.

  To be classified as a ‘spliceSite’ the variant must overlap with any portion of the first 2 or last 2 nucleotides in an intron.

  ‘intergenic’ variants are ranges that do not fall within a defined gene region. ‘transcripts by gene’ are extracted from the annotation and overlapped with the variant positions. Variants with no overlaps are classified as `intergenic`. When available, gene IDs for the flanking genes are provided as `PRECEDEID` and `FOLLOWID`. `upstream` and `downstream` arguments define the acceptable distance from the query for the flanking genes. `PRECEDEID` and `FOLLOWID` results are lists and contain all genes that fall within the defined distance. See the examples for how to compute the distance from ranges to PRECEDEID and FOLLOWID.

  ‘promoter’ variants fall within a specified range upstream and downstream of the transcription start site. Ranges values can be set with the `upstream` and `downstream` arguments when creating the `PromoterVariants()` or `AllVariants()` classes.

Subject as GRangesList:

  The `subject` can be a `TxDb` or `GRangesList` object. When using a `GRangesList` the type of data required is driven by the `VariantType` class. Below is a description of the appropriate `GRangesList` for each `VariantType`.

  CodingVariants:

    coding (CDS) by transcript

  IntronVariants:

    introns by transcript

  FiveUTRVariants:

    five prime UTR by transcript

  ThreeUTRVariants:

    three prime UTR by transcript

  IntergenicVariants:

    transcripts by gene

  SpliceSiteVariants:

    introns by transcript

  PromoterVariants:

    list of transcripts

  AllVariants:

    no GRangeList method available

Using the cache:

  When processing multiple VCF files performance is enhanced by specifying an environment as the `cache` argument. This cache is used to store and reuse extracted components of the subject (TxDb) required by the function. The first call to the function (i.e., processing the first VCF file in a list of many) populates the cache; repeated calls to `locateVariants` will access these objects from the cache vs re-extracting the same information.

### Value

A `GRanges` object with a row for each variant-transcript match. Strand of the output is from the `subject` hit except in the case of IntergenicVariants. For intergenic, multiple precede and follow gene ids are returned for each variant. When `ignore.strand=TRUE` the return strand is `*` because genes on both strands are considered and it is possible to have a mixture. When `ignore.strand=FALSE` the strand will match the `query` because only genes on the same strand are considered.

Metadata columns are `LOCATION`, `QUERYID`, `TXID`, `GENEID`, `PRECEDEID`, `FOLLOWID` and `CDSID`. Results are ordered by `QUERYID`, `TXID` and `GENEID`. Columns are described in detail below.

`LOCATION`

  Possible locations are ‘coding’, ‘intron’, ‘threeUTR’, ‘fiveUTR’, ‘intergenic’, ‘spliceSite’ and ‘promoter’.

  To be classified as ‘coding’, ‘intron’, ‘threeUTR’ or ‘fiveUTR’ the variant must fall completely within the region.

  ‘intergenic’ variants do not fall within a transcript. The ‘GENEID’ for these positions are `NA`. Lists of flanking genes that fall within the distance defined by `upstream` and `downstream` are given as ‘PRECEDEID’ and ‘FOLLOWID’. By default, the gene ID is returned in the ‘PRECEDEID’ and ‘FOLLOWID’ columns. To return the transcript ids instead set `idType = "tx"` in the `IntergenicVariants()` constructor.

  A ‘spliceSite’ variant overlaps any portion of the first 2 or last 2 nucleotides of an intron.

`LOCSTART, LOCEND`

  Genomic position in LOCATION-centric coordinates. If LOCATION is 'intron', these are intron-centric coordinates, if LOCATION is 'coding' then cds-centric. All coordinates are relative to the start of the transcript. SpliceSiteVariants, IntergenicVariants and PromoterVariants have no formal extraction 'by transcript' so for these variants LOCSTART and LOCEND are NA. Coordinates are computed with `mapToTranscripts`; see ?`mapToTranscripts` in the GenomicFeatures package for details.

`QUERYID`

  The `QUERYID` column provides a map back to the row in the original `query`. If the `query` was a `VCF` object this index corresponds to the row in the `GRanges` object returned by the `rowRanges` accessor.

`TXID`

  The transcript id taken from the `TxDb` object.

`CDSID`

  The coding sequence id(s) taken from the `TxDb` object.

`GENEID`

  The gene id taken from the `TxDb` object.

`PRECEDEID`

  IDs for all genes the query precedes within the defined `upstream` and `downstream` distance. Only applicable for ‘intergenic’ variants. By default this column contains gene ids; to return transcript ids set `idType = "tx"` in the `IntergenicVariants` constructor.

`FOLLOWID`

  IDs for all genes the query follows within the defined `upstream` and `downstream` distance. Only applicable for ‘intergenic’ variants. By default this column contains gene ids; to return transcript ids set `idType = "tx"` in the `IntergenicVariants` constructor.

All ID values will be ‘NA’ for variants with a location of `transcript_region` or `NA`.

### Author(s)

Valerie Obenchain

### See Also

- The readVcf function.

- The predictCoding function.

- The promoters function on the intra-range-methods man page in the GenomicRanges package.

### Examples

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

      ## ---------------------------------------------------------------------
      ## Variants in all gene regions
      ## ---------------------------------------------------------------------
      ## Read variants from a VCF file.
      fl <- system.file("extdata", "gl_chr1.vcf",
                        package="VariantAnnotation")
      vcf <- readVcf(fl, "hg19")

      ## Often the seqlevels in the VCF file do not match those in the TxDb.
      head(seqlevels(vcf))
      head(seqlevels(txdb))
      intersect(seqlevels(vcf), seqlevels(txdb))

      ## Rename seqlevels with renameSeqlevesl().
      vcf <- renameSeqlevels(vcf, paste0("chr", seqlevels(vcf)))

      ## Confirm.
      intersect(seqlevels(vcf), seqlevels(txdb))

      ## Overlaps for all possible variant locations.
      loc_all <- locateVariants(vcf, txdb, AllVariants())
      table(loc_all$LOCATION)

      ## ---------------------------------------------------------------------
      ## Variants in intergenic regions
      ## ---------------------------------------------------------------------
      ## Intergenic variants do not overlap a gene range in the
      ## annotation and therefore 'GENEID' is always NA. Flanking genes
      ## that fall within the 'upstream' and 'downstream' distances are
      ## reported as PRECEDEID and FOLLOWID.
      region <- IntergenicVariants(upstream=70000, downstream=70000)
      loc_int <- locateVariants(vcf, txdb, region)
      mcols(loc_int)[c("LOCATION", "PRECEDEID", "FOLLOWID")]

      ## Distance to the flanking genes can be computed for variants that
      ## have PRECEDEID(s) or FOLLOWID(s). Each variant can have multiple
      ## flanking id's so we first expand PRECEDEID and the corresponding
      ## variant ranges.
      p_ids <- unlist(loc_int$PRECEDEID, use.names=FALSE)
      exp_ranges <- rep(loc_int,  elementNROWS(loc_int$PRECEDEID))

      ## Compute distances with the distance method defined in GenomicFeatures.
      ## Help page can be found at ?`distance,GenomicRanges,TxDb-method`.
      ## The method returns NA for ids that cannot be collapsed into a single
      ## range (e.g., genes with ranges on multiple chromosomes).
      distance(exp_ranges, txdb, id=p_ids, type="gene")

      ## To search for distance by transcript id set idType='tx' in the
      ## IntergenicVariants() constructor, e.g.,
      ## locateVariants(vcf, txdb, region=IntergenicVariants(idType="tx"))

      ## Unlist ids and expand ranges as before to get p_ids and exp_ranges.
      ## Then call distance() with type = "tx":
      ## distance(exp_ranges, txdb, id=p_ids, type="tx")

      ## ---------------------------------------------------------------------
      ## GRangesList as subject
      ## ---------------------------------------------------------------------
      ## When 'subject' is a GRangesList the GENEID is unavailable and
      ## will always be reported as NA. This is because the GRangesList
      ## objects are extractions of region-by-transcript, not region-by-gene.
      ## Not run:
      cdsbytx <- cdsBy(txdb)
      locateVariants(vcf, cdsbytx, CodingVariants())

      intbytx <- intronsByTranscript(txdb)
      locateVariants(vcf, intbytx, IntronVariants())

    ## End(Not run)

      ## ---------------------------------------------------------------------
      ## Using the cache
      ## ---------------------------------------------------------------------
      ## When processing multiple VCF files, the 'cache' can be used
      ## to store the extracted components of the TxDb
      ## (i.e., cds by tx, introns by tx etc.). This avoids having to
      ## re-extract these GRangesLists during each loop.
      ## Not run:
      myenv <- new.env()
      files <- list(vcf1, vcf2, vcf3)
      lapply(files,
          function(fl) {
              vcf <- readVcf(fl, "hg19")
              ## modify seqlevels to match TxDb
              seqlevels(vcf_mod) <- paste0("chr", seqlevels(vcf))
              locateVariants(vcf_mod, txdb, AllVariants(), cache=myenv)
          })

    ## End(Not run)

      ## ---------------------------------------------------------------------
      ## Parallel implmentation
      ## ---------------------------------------------------------------------
      ## Not run:
      library(BiocParallel)

      ## A connection to a TxDb object is established when
      ## the package is loaded. Because each process reading from an
      ## sqlite db must have a unique connection the TxDb
      ## object cannot be passed as an argument when running in
      ## parallel. Instead the package must be loaded on each worker.

      ## The overhead of the multiple loading may defeat the
      ## purpose of running the job in parallel. An alternative is
      ## to instead pass the appropriate GRangesList as an argument.
      ## The details section on this man page under the heading
      ## 'Subject as GRangesList' explains what GRangesList is
      ## appropriate for each variant type.

      ## A. Passing a GRangesList:

      fun <- function(x, subject, ...)
          locateVariants(x, subject, IntronVariants())

      library(TxDb.Hsapiens.UCSC.hg19.knownGene)
      grl <- intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene)
      mclapply(c(vcf, vcf), fun, subject=grl)

      ## B. Passing a TxDb:

      ## Forking:
      ## In the case of forking, the TxDb cannot be loaded
      ## in the current workspace.
      ## To detach the NAMESPACE:
      ##     unloadNamespace("TxDb.Hsapiens.UCSC.hg19.knownGene")

      fun <- function(x) {
          library(TxDb.Hsapiens.UCSC.hg19.knownGene)
          locateVariants(x, TxDb.Hsapiens.UCSC.hg19.knownGene,
                         IntronVariants())
      }
      mclapply(c(vcf, vcf), fun)

      ## Clusters:
      cl <- makeCluster(2, type = "SOCK")
      fun <- function(query, subject, region) {
          library(VariantAnnotation)
          library(TxDb.Hsapiens.UCSC.hg19.knownGene)
          locateVariants(query, TxDb.Hsapiens.UCSC.hg19.knownGene, region)
      }
      parLapply(cl, c(vcf, vcf), fun, region=IntronVariants())
      stopCluster(cl)

    ## End(Not run)

[Package VariantAnnotation version 1.30.1 Index]