nearest-methods {GenomicFeatures} | R Documentation

## Finding the nearest genomic range neighbor in a TxDb

### Description

The `distance` methods for TxDb objects and subclasses.

### Usage

    ## S4 method for signature 'GenomicRanges,TxDb'
    distance(x, y, ignore.strand=FALSE,
        ..., id, type=c("gene", "tx", "exon", "cds"))

### Arguments

`x` | The query GenomicRanges instance.
`y` | For `distance`, a TxDb instance. The `id` is used to extract ranges from the TxDb which are then used to compute the distance from `x`.
`id` | A `character` vector the same length as `x`. The `id` must be identifiers in the TxDb object. `type` indicates what type of identifier `id` is.
`type` | A `character(1)` describing the `id`. Must be one of ‘gene’, ‘tx’, ‘exon’ or ‘cds’.
`ignore.strand` | A `logical` indicating if the strand of the ranges should be ignored. When `TRUE`, strand is set to `'+'`.
`...` | Additional arguments for methods.

### Details

- distance: Returns the distance for each range in `x` to the range extracted from the TxDb object `y`. Values in `id` are matched to one of ‘gene_id’, ‘tx_id’, ‘exon_id’ or ‘cds_id’ identifiers in the TxDb and the corresponding ranges are extracted. The `type` argument specifies which identifier is represented in `id`. The extracted ranges are used in the distance calculation with the ranges in `x`.

  The method returns `NA` values when the genomic region defined by `id` cannot be collapsed into a single range (e.g., when a gene spans multiple chromosomes) or if the `id` is not found in `y`.

  The behavior of `distance` with respect to zero-width ranges has changed in Bioconductor 2.12. See the man page `?distance` in IRanges for details.

### Value

For `distance`, an integer vector of distances between the ranges in `x` and `y`.

### Author(s)

Valerie Obenchain <vobencha@fhcrc.org>

### See Also

- nearest-methods man page in IRanges.

- nearest-methods man page in GenomicRanges.

### Examples

      ## -----------------------------------------------------------
      ## distance()
      ## -----------------------------------------------------------

      library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
      txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
      gr <- GRanges(c("chr2L", "chr2R"),
                    IRanges(c(100000, 200000),  width=100))
      distance(gr, txdb, id=c("FBgn0259717", "FBgn0261501"), type="gene")
      distance(gr, txdb, id=c("10000", "23000"), type="cds")

      ## The id's must be in the appropriate order with respect to 'x'.
      distance(gr, txdb, id=c("4", "4097"), type="tx")

      ## 'id' "4" is on chr2L and "4097" is on chr2R.
      transcripts(txdb, filter=list(tx_id=c("4", "4097")))

      ## If we reverse the 'id' the chromosomes are incompatable with gr.
      distance(gr, txdb, id=c("4097", "4"), type="tx")

      ## distance() compares each 'x' to the corresponding 'y'.
      ## If an 'id' is not found in the TxDb 'y' will not
      ## be the same lenth as 'x' and an error is thrown.
      ## Not run:
      distance(gr, txdb, id=c("FBgn0000008", "INVALID"), type="gene") ## will fail

    ## End(Not run)

[Package GenomicFeatures version 1.40.1 Index]