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The output from proteinToGenome has empty value #157
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I tried with current Bioconductor package versions (3.19) and Ensembl release 112 and it seems to work: library(ensembldb)
library(AnnotationHub)
edb <- ah[["AH116860"]]
rng <- IRanges(start = 1, end = 28)
names(rng) <- "ENSP00000518892"
proteinToGenome(rng, edb)
Fetching CDS for 1 proteins ... 1 found
Checking CDS and protein sequence lengths ... 1/1 OK
$ENSP00000518892
GRanges object with 1 range and 7 metadata columns:
seqnames ranges strand | protein_id tx_id
<Rle> <IRanges> <Rle> | <character> <character>
[1] 5 179644937-179645020 - | ENSP00000518892 ENST00000511063
exon_id exon_rank cds_ok protein_start protein_end
<character> <integer> <logical> <integer> <integer>
[1] ENSE00003874488 1 TRUE 1 28
-------
seqinfo: 1 sequence from GRCh38 genome
maybe you used a different Ensembl release? |
I stumbled over this yesterday too: The reason was that it wasn't obvious to me that the ranges need to have protein ID names. The names are set in the Examples section of
|
thanks for the comment @mschubert ! When you write
do you mean the help page of the Regarding the second point, yes that makes sense. I'll look into it - and see if that has no other unwanted effects. |
@mschubert This is quite unexpected... I've never thought about this before. Thank you! |
- Improve documentation of `proteinToGenome()` describing the input parameter better. - Throw error if provided `IRanges` does not contain protein identifiers.
- Improve `proteinToGenome()` documentation. - Check input parameters of `proteinToGenome()` to ensure protein identifiers were provided (issue #157).
Yes, exactly. I see you already added that, great, thank you! |
I'm closing this issue now - feel free to reopen if needed. |
As an example, I would like to map the 1-28 amino acid of
ENSP00000518892
back to its genomic coordinates. According tobiomaRt
query result, the respective transcript sequence should be:The peptide sequence is as below:
But I cannot get this query from the
proteinToGenome
output. It returns an empty record:May I ask why this happens? I don't understand why the sequence can all be found in the Ensembl database but cannot be mapped using
proteinToGenome
.Thank you.
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