1
$\begingroup$

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?

Improve this question
$\endgroup$
5
  • $\begingroup$ You can install a new version of R without a new OS. Which problem are you having? When I try your code the problem is that j is not defined, if I define it with a number I get unable to find an inherited method for function ‘XString’ for signature ‘"integer"’ (and I'm using the latest versions of Bioconductor and R) $\endgroup$
    – llrs
    Dec 25 '18 at 16:19
  • $\begingroup$ Sorry, I had extracted that line from a loop and forgot to change the j. Should work now. I have a 5 year old computer and the OSX version I was using wouldn't allow upgrading R. I ended up upgrading my OSX version and reinstalling R. I'll see if it works now. $\endgroup$
    – Will Gibson
    Dec 25 '18 at 18:52
  • $\begingroup$ It doesn't work, I said so in my previous comment, see the error, and could you explain what are you doing in this long line? $\endgroup$
    – llrs
    Dec 25 '18 at 19:35
  • 1
    $\begingroup$ You are simply using a substr command, which is present in Perl and there is a very cool way for doing this in python. It is honestly easier to code this directly. $\endgroup$
    – M__
    Dec 26 '18 at 13:25
  • $\begingroup$ From what I heard even learning R is kinda waste of time, much less using it for simple scripts. $\endgroup$
    – Mithoron
    Jan 3 '19 at 23:24
2
$\begingroup$

It turned out that I needed to reinstall OSX to upgrade my R version and biomaRt install.

Improve this answer
$\endgroup$
2
$\begingroup$

You could also save your "biomart_query_result" object after the first time it is generated. Then you can re-use it without having to depend on the biomaRt API functionality.

Improve this answer
$\endgroup$
1
$\begingroup$

Would this be useful to you?


   library(EnsDb.Hsapiens.v86)  
   library(ensembldb)
   mygene <- genes(EnsDb.Hsapiens.v86, filter= GenenameFilter("KRAS"))

to get the protein info and protein sequence for each transcript

proteins(EnsDb.Hsapiens.v86, filter= GenenameFilter("KRAS"))

Also have a look at functions proteinToTranscript proteinToGenome

> x<- proteins(EnsDb.Hsapiens.v86, filter= GenenameFilter("KRAS"), return.type = "AAStringSet")
> x
  A AAStringSet instance of length 4
    width seq                                    names               
[1]   188 MTEYKLVVVGAGGVGKSA...KDGKKKKKKSKTKCVIM ENSP00000308495
[2]    75 MTEYKLVVVGAGGVGKSA...KDGKKKKKKSKTKCVIM ENSP00000452512
[3]   189 MTEYKLVVVGAGGVGKSA...KEEKTPGCVKIKKCIIM ENSP00000256078
[4]    43 MTEYKLVVVGAGGVGKSA...HFVDEYDPTIEVLLSSM ENSP00000451856

There are also functions exons, exonsBy, transcriptsBy, cdsBy, fiveUTRsByTranscript and threeUTRsByTranscript. These functions return a GenomicRanges object and inherit all of the methods in that package too. 

x<-  genes(EnsDb.Hsapiens.v86, filter= GenenameFilter("KRAS"))
start(x)
end(x)
strand(x)
length(x)
flank(x)

You can manipulate the sequence selected as an IRanges object

ranges(x)   # gives an IRanges object
narrow(ranges(x), start=10, end=20)  # select the 10th position 

> ranges(x)
IRanges object with 1 range and 0 metadata columns:
                      start       end     width
                  <integer> <integer> <integer>
  ENSG00000133703  25204789  25250936     46148
> narrow(ranges(x), start=10, end=19)
IRanges object with 1 range and 0 metadata columns:
                      start       end     width
                  <integer> <integer> <integer>
  ENSG00000133703  25204798  25204807        10

It is worth having a look at these vignettes. Let me know if you've questions or post to the Bioconductor support forum ;-)

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.