proteinToTranscript {ensembldb} | R Documentation

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

### Description

`proteinToTranscript` maps protein-relative coordinates to positions within the encoding transcript. Note that the returned positions are relative to the complete transcript length, which includes the 5' UTR.

Similar to the `proteinToGenome()` function, `proteinToTranscript` compares for each protein whether the length of its sequence matches the length of the encoding CDS and throws a warning if that is not the case. Incomplete 3' or 5' CDS of the encoding transcript are the most common reasons for a mismatch between protein and transcript sequences.

### Usage

    proteinToTranscript(x, db, id = "name", idType = "protein_id")

### Arguments

`x` | `IRanges` with the coordinates within the protein(s). The object has also to provide some means to identify the protein (see details).
`db` | `EnsDb` object to be used to retrieve genomic coordinates of encoding transcripts.
`id` | `character(1)` specifying where the protein identifier can be found. Has to be either `"name"` or one of `colnames(mcols(prng))`.
`idType` | `character(1)` defining what type of IDs are provided. Has to be one of `"protein_id"` (default), `"uniprot_id"` or `"tx_id"`.

### Details

Protein identifiers (supported are Ensembl protein IDs or Uniprot IDs) can be passed to the function as `names` of the `x` `IRanges` object, or alternatively in any one of the metadata columns (`mcols`) of `x`.

### Value

`IRangesList`, each element being the mapping results for one of the input ranges in `x`. Each element is a `IRanges` object with the positions within the encoding transcript (relative to the start of the transcript, which includes the 5' UTR). The transcript ID is reported as the name of each `IRanges`. The `IRanges` can be of length > 1 if the provided protein identifier is annotated to more than one Ensembl protein ID (which can be the case if Uniprot IDs are provided). If the coordinates can not be mapped (because the protein identifier is unknown to the database) an `IRanges` with negative coordinates is returned.

The following metadata columns are available in each `IRanges` in the result:

- `"protein_id"`: the ID of the Ensembl protein for which the within-protein coordinates were mapped to the genome.

- `"tx_id"`: the Ensembl transcript ID of the encoding transcript.

- `"cds_ok"`: contains `TRUE` if the length of the CDS matches the length of the amino acid sequence and `FALSE` otherwise.

- `"protein_start"`: the within-protein sequence start coordinate of the mapping.

- `"protein_end"`: the within-protein sequence end coordinate of the mapping.

### Note

While mapping of Ensembl protein IDs to Ensembl transcript IDs is 1:1, a single Uniprot identifier can be annotated to several Ensembl protein IDs. `proteinToTranscript` calculates in such cases transcript-relative coordinates for each annotated Ensembl protein.

Mapping using Uniprot identifiers needs also additional internal checks that can have a significant impact on the performance of the function. It is thus strongly suggested to first identify the Ensembl protein identifiers for the list of input Uniprot identifiers (e.g. using the `proteins()` function and use these as input for the mapping function.

### Author(s)

Johannes Rainer

### See Also

Other coordinate mapping functions: `cdsToTranscript`, `genomeToProtein`, `genomeToTranscript`, `proteinToGenome`, `transcriptToCds`, `transcriptToGenome`, `transcriptToProtein`

### Examples

    library(EnsDb.Hsapiens.v86)
    ## Restrict all further queries to chromosome x to speed up the examples
    edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "X")

    ## Define an IRange with protein-relative coordinates within a protein for
    ## the gene SYP
    syp <- IRanges(start = 4, end = 17)
    names(syp) <- "ENSP00000418169"
    res <- proteinToTranscript(syp, edbx)
    res
    ## Positions 4 to 17 within the protein span are encoded by the region
    ## from nt 23 to 64.

    ## Perform the mapping for multiple proteins identified by their Uniprot
    ## IDs.
    ids <- c("O15266", "Q9HBJ8", "unexistant")
    prngs <- IRanges(start = c(13, 43, 100), end = c(21, 80, 100))
    names(prngs) <- ids

    res <- proteinToTranscript(prngs, edbx, idType = "uniprot_id")

    ## The result is a list, same length as the input object
    length(res)
    names(res)

    ## No protein/encoding transcript could be found for the last one
    res[[3]]

    ## The first protein could be mapped to multiple Ensembl proteins. The
    ## region within all transcripts encoding the region in the protein are
    ## returned
    res[[1]]

    ## The result for the region within the second protein
    res[[2]]

[Package ensembldb version 2.6.8 Index]