Map transcript-relative coordinates to amino acid residues of the encoded protein

transcriptToProtein maps within-transcript coordinates to the corresponding coordinates within the encoded protein sequence. The provided coordinates have to be within the coding region of the transcript (excluding the stop codon) but are supposed to be relative to the first nucleotide of the transcript (which includes the 5' UTR). Positions relative to the CDS of a transcript (e.g. /PKP2 c.1643delg/) have to be first converted to transcript-relative coordinates. This can be done with the cdsToTranscript() function.

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

Arguments

x

IRanges with the coordinates within the transcript. Coordinates are counted from the start of the transcript (including the 5' UTR). 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 protein sequence, names being the (Ensembl) IDs of the protein. The original transcript ID and the transcript-relative coordinates are provided as metadata columns. Metadata columns "cds_ok" indicates whether the length of the transcript's CDS matches the length of the encoded protein. IRanges with a start coordinate of -1 is returned for transcript coordinates that can not be mapped to protein-relative coordinates (either no transcript was found for the provided ID, the transcript does not encode a protein or the provided coordinates are not within the coding region of the transcript).

Details

Transcript-relative coordinates are mapped to the amino acid residues they encode. As an example, positions within the transcript that correspond to nucleotides 1 to 3 in the CDS are mapped to the first position in the protein sequence (see examples for more details).

See also

cdsToTranscript() and transcriptToCds() for conversion between CDS- and transcript-relative coordinates.

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

Author

Johannes Rainer

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 IRanges with the positions of the first 2 nucleotides of the
## coding region for the transcript ENST00000381578
txpos <- IRanges(start = 692, width = 2, names = "ENST00000381578")

## Map these to the corresponding residues in the protein sequence
## The protein-relative coordinates are returned as an `IRanges` object,
## with the original, transcript-relative coordinates provided in metadata
## columns tx_start and tx_end
transcriptToProtein(txpos, edbx)
#> IRanges object with 1 range and 4 metadata columns:
#>                       start       end     width |           tx_id  tx_start
#>                   <integer> <integer> <integer> |     <character> <integer>
#>   ENSP00000370990         1         1         1 | ENST00000381578       692
#>                      tx_end    cds_ok
#>                   <integer> <logical>
#>   ENSP00000370990       693      TRUE

## We can also map multiple ranges. Note that for any of the 3 nucleotides
## encoding the same amino acid the position of this residue in the
## protein sequence is returned. To illustrate this we map below each of the
## first 4 nucleotides of the CDS to the corresponding position within the
## protein.
txpos <- IRanges(start = c(692, 693, 694, 695),
    width = rep(1, 4), names = rep("ENST00000381578", 4))
transcriptToProtein(txpos, edbx)
#> IRanges object with 4 ranges and 4 metadata columns:
#>                       start       end     width |           tx_id  tx_start
#>                   <integer> <integer> <integer> |     <character> <integer>
#>   ENSP00000370990         1         1         1 | ENST00000381578       692
#>   ENSP00000370990         1         1         1 | ENST00000381578       693
#>   ENSP00000370990         1         1         1 | ENST00000381578       694
#>   ENSP00000370990         2         2         1 | ENST00000381578       695
#>                      tx_end    cds_ok
#>                   <integer> <logical>
#>   ENSP00000370990       692      TRUE
#>   ENSP00000370990       693      TRUE
#>   ENSP00000370990       694      TRUE
#>   ENSP00000370990       695      TRUE

## If the mapping fails, an IRanges with negative start position is returned.
## Mapping can fail (as below) because the ID is not known.
transcriptToProtein(IRanges(1, 1, names = "unknown"), edbx)
#> Warning: Transcript(s) 'unknown' could not be found
#> IRanges object with 1 range and 4 metadata columns:
#>           start       end     width |       tx_id  tx_start    tx_end    cds_ok
#>       <integer> <integer> <integer> | <character> <integer> <integer> <logical>
#>   [1]        -1        -1         1 |     unknown         1         1      <NA>

## Or because the provided coordinates are not within the CDS
transcriptToProtein(IRanges(1, 1, names = "ENST00000381578"), edbx)
#> Warning: Provided coordinates for 'ENST00000381578' are not within the coding region
#> IRanges object with 1 range and 4 metadata columns:
#>           start       end     width |           tx_id  tx_start    tx_end
#>       <integer> <integer> <integer> |     <character> <integer> <integer>
#>   [1]        -1        -1         1 | ENST00000381578         1         1
#>          cds_ok
#>       <logical>
#>   [1]      <NA>