Map transcript-relative coordinates to positions within the CDS
Converts transcript-relative coordinates to positions within the CDS (if the transcript encodes a protein).
transcriptToCds(x, db, id = "name")
x |
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db |
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id |
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IRanges with the same length (and order) than the input IRanges
x. Each element in IRanges provides the coordinates within the
transcripts CDS. The transcript-relative coordinates are provided
as metadata columns.
IRanges with a start coordinate of -1 is returned for transcripts
that are not known in the database, non-coding transcripts or if the
provided start and/or end coordinates are not within the coding region.
Johannes Rainer
Other coordinate mapping functions:
cdsToTranscript(),
genomeToProtein(),
genomeToTranscript(),
proteinToGenome(),
proteinToTranscript(),
transcriptToGenome(),
transcriptToProtein()
library(EnsDb.Hsapiens.v86)
## Defining transcript-relative coordinates for 4 transcripts of the gene
## BCL2
txcoords <- IRanges(start = c(1463, 3, 143, 147), width = 1,
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955"))
## Map the coordinates.
transcriptToCds(txcoords, EnsDb.Hsapiens.v86)
## ENST00000590515 does not encode a protein and thus -1 is returned
## The coordinates within ENST00000333681 are outside the CDS and thus also
## -1 is reported.Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.