nearest-methods: Finding the nearest genomic range neighbor in a TxDb

Description Usage Arguments Details Value Author(s) See Also Examples

Description

The distance methods for TxDb objects and subclasses.

Usage

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## 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

Value

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

Author(s)

Valerie Obenchain <vobencha@fhcrc.org>

See Also

Examples

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  ## -----------------------------------------------------------
  ## 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) 

Bioconductor/GenomicFeatures documentation built on May 25, 2021, 5:47 a.m.