annmap coding functions

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Description

Functions to deal with coding regions and UTRs

Usage

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  transcriptToUtrRange( ids, end=c( "both", "5", "3" ), as.data.frame=FALSE, on.translation.error=stop )
  transcriptToUtrExon( ids, end=c( 'both', '5', '3' ), as.vector=FALSE, on.translation.error=stop )
  transcriptToCodingRange( ids, end=c( "both", "5", "3" ), as.data.frame=FALSE, on.translation.error=stop )
  transcriptToCodingExon( ids, end=c( 'both', '5', '3' ), as.vector=FALSE, on.translation.error=stop )
  utrProbesets( probesets, transcripts, end=c( "both", "5", "3" ), on.translation.error=stop )
  codingProbesets( probesets, transcripts, end=c( "both", "5", "3" ), on.translation.error=stop )
  nonIntronicTranscriptLength( ids, end=c( 'none', 'both', '5', '3' ), on.translation.error=stop )
  nonIntronicGeneLength( ids )

Arguments

ids

A vector of Transcript Names, or a RangedData object of Transcripts returned from another annmap call.

as.data.frame

If FALSE, data will be converted to a RangedData object if possible, otherwise a data.frame

as.vector

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

probesets

An optional vector of Probeset Names, or a RangedData object of Probesets returned from another annmap call.

transcripts

An optional vector of Transcript Names, or a RangedData object of Transcripts returned from another annmap call.

end

Which end ("both", "3" or "5") of the Transcript(s) you are interested in (defaults to both).

on.translation.error

A function to call with a character vector explaining the problem if one is encountered with the translation locations in the database.

Details

The first two functions given here, transcriptToUtrRange and transcriptToCodingRange return the transcripts of interest, with their ranges adjusted depending on the UTR of each.

With transcriptToUtrRange, a RangedData object is returned with the name of the transcript, the end in question, and the genomic location of that UTR. If both is passed as the end parameter, then each transcript will generate up to two rows in the returned object. It may return less than two rows if the end parameter is used, or if there is no UTR for the end specified. (A Transcript with no UTR will return zero results)

The transcriptToCodingRange function returns the same as calling transcriptDetails, but with the start and end locations modified by the range of the UTR. If end is passed, then only the UTR at this end will be taken into consideration and used to modify the returned location.

The transcriptToCodingExon and transcriptToUtrExon functions return the exons for each transcript limited to only those exons (or partions thereof) which are coding or part of the UTR.

utrProbesets and codingProbesets are functions to find or filter probesets which have probes targeting the type of region specified by the function name.

A call to utrProbesets with a list of Probesets will return those probesets that have at least one probe hitting the UTR of any transcript.

A call to utrProbesets with a list of Probesets and a list of Transcripts will return those probesets the have at least one probe hitting the UTR of any of the specified Transcripts.

A call to utrProbesets with only the probesets parameter omitted, will return all probesets which have at least one probe in the UTR region of the specified Transcripts.

You cannot omit both the Probesets and Transcripts parameters simultaneously.

The codingProbesets method does the inverse of the utrProbesets function: it returns probesets having at least one probe in the coding region of a Transcipt (or the specified Transcripts).

Note that the UTR of a Transcript includes the intronic UTR regions, and the coding region of a Transcript includes the intronic coding regions.

This means that utrProbesets and codingProbesets can sometimes return intronic and/or intergenic probesets. These can be removed with a call to the appropriate filter function (see examples).

All unreliable probesets are automatically removed by these functions before mapping.

Calling nonIntronicTranscriptLength will return the length of the exons (coding can be specified via the end parameter) in a given list of transcripts.

And nonIntronicGeneLength will give the length of all exons in a given gene when overlaps are taken into account (so two exactly overlapping exons will count once for the length)

Author(s)

Tim Yates

See Also

annmapTo
annmapDetails
annmapAll
annmapRange
annmapFilters

Examples

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  if(interactive()) {
    # Only return exonic probesets hitting the UTRs of ENST00000414566
    exonic( utrProbesets( NULL, "ENST00000414566" ) )
  }