cdsToTranscript: Map positions within the CDS to coordinates relative to the...

In jotsetung/ensembldb: Utilities to create and use Ensembl-based annotation databases

Map positions within the CDS to coordinates relative to the start of the transcript

Description

Converts CDS-relative coordinates to positions within the transcript, i.e. relative to the start of the transcript and hence including its 5' UTR.

Usage

cdsToTranscript(x, db, id = "name", exons = NA, transcripts = NA)

Arguments

x	IRanges with the coordinates within the CDS. Coordinates are expected to be relative to the transcription start (the first nucleotide of the transcript). The Ensembl IDs of the corresponding transcripts have to be provided either as names of the IRanges, or in one of its metadata columns.
db	EnsDb object.
id	character(1) specifying where the transcript identifier can be found. Has to be either "name" or one of colnames(mcols(prng)).
exons	CompressedGRangesList object generated by exonsBy() where by = 'tx'.
transcripts	GRanges object generated by transcripts().

Value

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.

Author(s)

Johannes Rainer

See Also

Other coordinate mapping functions: genomeToProtein(), genomeToTranscript(), proteinToGenome(), proteinToTranscript(), transcriptToCds(), transcriptToGenome(), transcriptToProtein()

Examples

library(EnsDb.Hsapiens.v86)
## Defining transcript-relative coordinates for 4 transcripts of the gene
## BCL2
txcoords <- IRanges(start = c(4, 3, 143, 147), width = 1,
    names = c("ENST00000398117", "ENST00000333681",
    "ENST00000590515", "ENST00000589955"))

cdsToTranscript(txcoords, EnsDb.Hsapiens.v86)

## Next we map the coordinate for variants within the gene PKP2 to the
## genome. The variants is PKP2 c.1643DelG and the provided
## position is thus relative to the CDS. We have to convert the
## position first to transcript-relative coordinates.
pkp2 <- IRanges(start = 1643, width = 1, name = "ENST00000070846")

## Map the coordinates by first converting the CDS- to transcript-relative
## coordinates
transcriptToGenome(cdsToTranscript(pkp2, EnsDb.Hsapiens.v86),
    EnsDb.Hsapiens.v86)

## Meanwhile, this function can be called in parallel processes if you preload
## the exons and transcripts database.

exons <- exonsBy(EnsDb.Hsapiens.v86)
transcripts <- transcripts(EnsDb.Hsapiens.v86)

cdsToTranscript(txcoords, EnsDb.Hsapiens.v86, exons = exons,transcripts = transcripts)

jotsetung/ensembldb documentation built on Aug. 21, 2024, 11:23 a.m.