annmap coding functions
Functions to deal with coding regions and UTRs
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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 )
A vector of Transcript Names, or a RangedData object of Transcripts returned from another annmap call.
An optional vector of Probeset Names, or a RangedData object of Probesets returned from another annmap call.
An optional vector of Transcript Names, or a RangedData object of Transcripts returned from another annmap call.
Which end (
A function to call with a character vector explaining the problem if one is encountered with the translation locations in the database.
The first two functions given here,
transcriptToCodingRange return the transcripts
of interest, with their ranges adjusted depending on the UTR of each.
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)
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.
transcriptToUtrExon functions return the exons for each transcript limited to only those exons (or partions thereof) which are coding or part of the UTR.
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.
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
codingProbesets can sometimes return
These can be removed with a call to the appropriate filter function (see examples).
unreliable probesets are automatically removed by these functions before mapping.
nonIntronicTranscriptLength will return the length of the exons (coding can be specified via the
end parameter) in a given list of transcripts.
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)
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