R: Finding the nearest genomic range neighbor in a TranscriptDb

nearest-methods {GenomicFeatures}

R Documentation

Finding the nearest genomic range neighbor in a TranscriptDb

Description

The distance methods for TranscriptDb objects and subclasses.

Usage

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

Arguments

`x`	The query GenomicRanges instance.
`y`	For `distance`, a TranscriptDb instance. The `id` is used to extract ranges from the TranscriptDb 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 TranscriptDb 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 TranscriptDb object y. Values in id are matched to one of ‘gene_id’, ‘tx_id’, ‘exon_id’ or ‘cds_id’ identifiers in the TranscriptDb 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 behavior of distance 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>

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, 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 TranscriptDb '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 1.14.2 Index]