annmap
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

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annmap.range: annmap 'range' functions

annmap.range: annmap 'range' functions
In annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

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

Description

Get the features within the specified genome coordinates.

Usage

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  domainInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
domainInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
domainInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
domainInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
domainInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
domainInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
domainInRange( x, start, end, strand, ..., as.vector=FALSE )

  estExonInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
estExonInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
estExonInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
estExonInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
estExonInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
estExonInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
estExonInRange( x, start, end, strand, ..., as.vector=FALSE )

  estGeneInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
estGeneInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
estGeneInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
estGeneInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
estGeneInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
estGeneInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
estGeneInRange( x, start, end, strand, ..., as.vector=FALSE )

  estTranscriptInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
estTranscriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
estTranscriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
estTranscriptInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
estTranscriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
estTranscriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
estTranscriptInRange( x, start, end, strand, ..., as.vector=FALSE )

  exonInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
exonInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
exonInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
exonInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
exonInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
exonInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
exonInRange( x, start, end, strand, ..., as.vector=FALSE )

  geneInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
geneInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
geneInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
geneInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
geneInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
geneInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
geneInRange( x, start, end, strand, ..., as.vector=FALSE )

  predictionTranscriptInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
predictionTranscriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
predictionTranscriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
predictionTranscriptInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
predictionTranscriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
predictionTranscriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
predictionTranscriptInRange( x, start, end, strand, ..., as.vector=FALSE )

  probesetInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
probesetInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
probesetInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
probesetInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
probesetInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
probesetInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
probesetInRange( x, start, end, strand, ..., as.vector=FALSE )

  probeInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
probeInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
probeInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
probeInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
probeInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
probeInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
probeInRange( x, start, end, strand, ..., as.vector=FALSE )

  proteinInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
proteinInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
proteinInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
proteinInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
proteinInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
proteinInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
proteinInRange( x, start, end, strand, ..., as.vector=FALSE )

  transcriptInRange( x, ..., as.vector = FALSE )
  ## S4 method for signature 'GRanges'
transcriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'RangedData'
transcriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'character'
transcriptInRange( x, start, end, strand, ..., as.vector=FALSE )
  ## S4 method for signature 'data.frame'
transcriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'NULL'
transcriptInRange( x, as.vector=FALSE )
  ## S4 method for signature 'factor'
transcriptInRange( x, start, end, strand, ..., as.vector=FALSE )

Arguments

as.vector

If TRUE returns a vector of database identifiers. If FALSE returns a GRanges object containing detailed annotation.

x

The name of the chromosome of interest – in the case of the factor or character variants), or a GRanges object or data.frame containing location information. In the case of a data.frame, columns must be named chr or chromosome_name, followed by start, end and strand. RangedData objects must contain a strand in their meta-data. And strand must be 1 or -1 in all cases arart from GRanges where it obviously has to be + or -. All of the NULL variants simply return NULL, in-keeping with the fluent style of the rest of the package.

start

Start of the region

end

End of the region

strand

1 == top stand, -1 == bottom strand

...

The ellipsis is to allow this multi-method style of programming.

Details

Find all the specified features within a given region of the genome. For all functions except probeInRange, features that fall on the boundaries of the region (i.e. are partially overlapping) are returned too. For probeInRange probes that span the start of the range are NOT returned (but those spanning the end of the range are).

The function annmapRangeApply makes it possible to map any of these functions down the rows of a RangedData or GRanges object. The defaults are set up so that it will handle the output of one of the InRange methods here. This makes it easy to nest functions, for example, to find all genes in a given region of the the genome, and then find the exon array probes that map to those genes (see below).

Value

Returns a GRanges object, one \'row\' per feature, containing detailed annotations, or a vector of identifiers, depending on the value of as.vector.

Author(s)

Tim Yates

See Also

annmapTo
annmapDetails
annmapAll
annmapUtils
annmapFilters
RangedData GRanges

Examples

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  if(interactive()) {
    annmapConnect()

    r = geneInRange( '17', 7510000, 7550000, 1 )

    # Can take equal length vectors as parameters
    geneInRange( c( '17', 'X' ), c( 7510000, 1000000 ), c( 7550000, 1500000 ), c( -1, -1 ) )

    # Or a data.frame
    df = data.frame( chr=c( '17', 'X' ), start=c( 7510000, 1000000 ), end=c( 7550000, 1500000 ), strand=c( -1, -1 ) )
    geneInRange( df )

    # Or RangedData objects
    transcriptInRange( geneDetails( symbolToGene( c( 'tp53', 'ssh' ) ) ) )
  }

annmap documentation built on Nov. 8, 2020, 7:43 p.m.

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