transcriptToCds {ensembldb} | R Documentation

## Map transcript-relative coordinates to positions within the CDS

### Description

Converts transcript-relative coordinates to positions within the CDS (if the transcript encodes a protein).

### Usage

    transcriptToCds(x, db, id = "name")

### Arguments

`x` | `IRanges` with the coordinates within the transcript. 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))`.

### 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: `cdsToTranscript`, `genomeToProtein`, `genomeToTranscript`, `proteinToGenome`, `proteinToTranscript`, `transcriptToGenome`, `transcriptToProtein`

### Examples

    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.

[Package ensembldb version 2.6.8 Index]