I'm trying to find the amino acid context around a particular position in a protein (5 aa amino acid window on each side).
I used to have some code that works and then biomaRt stopped working. I think some of these issues would be fixed in later versions of biomaRt, but I would have to install a new version of R, which would require me to install a new version of my OS.
require('biomaRt')
require('Biostrings')
hs_ensembl_mart =
useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl")
gene_names=c('KRAS')
aa_affected_loc=12
biomart_query_results=getBM(attributes=c('hgnc_symbol', 'entrezgene','coding'),
filters = 'hgnc_symbol',
values = gene_names,
mart = hs_ensembl_mart)
preceding_peptide= substr(as.character(translate(DNAString(biomart_query_results[1,'coding']))),aa_affected_loc-5,aa_affected_loc-1)
trailing_peptide= substr(as.character(translate(DNAString(biomart_query_results[1,'coding']))),aa_affected_loc+1,aa_affected_loc+5)
Does anyone have a workaround for this?
j
is not defined, if I define it with a number I getunable to find an inherited method for function ‘XString’ for signature ‘"integer"’
(and I'm using the latest versions of Bioconductor and R) $\endgroup$