The function dissects transcribed regions (transcripts) genome-wide and performs expression level quantification.
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The function uses two parameters to identify transcribed regions:
gap.dist as calculated by the
respectively and stored in the
Alternatively, the user may specify his/her own values to be passed to
the function. By increasing the
gap.dist, fewer transcripts of
longer size will be identified, and an increase in the
will result in fewer transcripts of shorter size (a typical transcript tends
to have a lower fragments coverage at the 3' end, and thus, the
coverage.cutoff value will have an impact on the resulting length of
the detected transcript).
estimate.params is set TRUE, the following metrics are estimated for
length- transcript length (in base pairs).
bases.covered- the number of bases covered by the sequencing fragments.
coverage- the proportion of transcript length covered by fragments. Value in the range (0, 1].
fragments- total number of fragments per transcript.
fpkm- Fragments Per Kilobase of transcript per Million mapped reads.
coverage is a measure of how densely the transcript is covered by
the sequencing fragments. Modestly/highly expressed transcripts will have
a value close to 1, whereas lowly expressed transcripts will have a
value close to 0, indicating the sparse distribution of sequencing
fragments along the transcript body.
transcripts of the provided
TranscriptionDataSet object will be updated by the
GRanges object, containing detected
transcripts and, if estimated, corresponding expression levels.
Armen R. Karapetyan
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### Load TranscriptionDataSet object data(tds) ### Load reference annotations (knownGene from UCSC) data(annot) ### Detect transcripts detectTranscripts(object = tds, coverage.cutoff = 5, gap.dist = 4000, estimate.params = TRUE, combine.by.annot = FALSE, annot = annot) ### View detected transcripts getTranscripts(tds)