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ORF lengths using Yeast Annotation package

Hi,

I am trying to find out length of Yeast ORF. Where is my mistake?

> sacCer3Length <- function(symbols)
  {
  require(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
  require(org.Sc.sgd.db)
  exons.db = exonsBy(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, by='gene')
  egs    = unlist(  mget(symbols[ symbols %in% keys(org.Sc.sgd) ],org.Sc.sgd) )
  sapply(egs,function(eg)
  {
  exons = exons.db[[eg]]
  exons = reduce(exons)
  sum( width(exons) )
  })
  }

> sacCer3Length('YNL079C')

Error in unlist(mget(symbols[symbols %in% keys(org.Sc.sgd)], org.Sc.sgd)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in mget(symbols[symbols %in% keys(org.Sc.sgd)], org.Sc.sgd) : 
  error in evaluating the argument 'x' in selecting a method for function 'mget': Error in symbols %in% keys(org.Sc.sgd) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'keys' for signature '"function"'

Regards,
Deepak

bioconductor r
• 3,058 views • link
updated by Ram Ram • written by dktarathym • dktarathym

Don't yeast have alternatively spliced genes? If so, getting exons by gene, reduce()ing that and then summing the exons won't work. Also, UTRs will mess that up.

• 0 views • link
written by Devon Ryan Devon Ryan

Should I use:

exons.db = cdsBy(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, by='gene')

• 0 views • link
written by dktarathym • dktarathym

That'll at least solve the UTR issue, though it'll still miss alternative splicing. The general idea is to pull out CDS for a gene and then calculate from that the ORF length of each transcript. You then return the longest ORF length (or the mean, or median, or...). Not calculating by transcript will often over-estimate things in cases where there's more than pure exon skipping.

• 0 views • link
written by Devon Ryan Devon Ryan 
> sacCer3Length <- function(symbols)
+ {
+ require(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
+ require(org.Sc.sgd.db)
+ exons.db = transcriptsBy(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, by='gene')
+ egs    = unlist(get(symbols[symbols %in% keys(org.Sc.sgd)],org.Sc.sgd))
+ sapply(egs,function(eg)
+ {
+ exons = exons.db[[eg]]
+ exons = reduce(exons)
+ sum( width(exons) )
+ })
+ }
> sacCer3Length('YNL079C')
Error in unlist(get(symbols[symbols %in% keys(org.Sc.sgd)], org.Sc.sgd)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in get(symbols[symbols %in% keys(org.Sc.sgd)], org.Sc.sgd) : 
  error in evaluating the argument 'x' in selecting a method for function 'get': Error in symbols %in% keys(org.Sc.sgd) : 
  error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'keys' for signature '"function"'

Problem is in code (I believe): egs = unlist(get(symbols[symbols %in% keys(org.Sc.sgd)],org.Sc.sgd))

• 0 views • link
updated by Ram Ram • written by dktarathym • dktarathym

Yes, the problem in the code can be deduced from

error in evaluating the argument 'table' in selecting a method for function '%in%': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘keys’ for signature ‘"function"’

You probably want org.Sc.sgdGENENAME or something like that rather than org.Sc.sgd.

Note that your ORFs are still wrong, though.

• 0 views • link
written by Devon Ryan Devon Ryan

I have ORF. I want to make a function, that will return the length of these ORF.

• 0 views • link
written by dktarathym • dktarathym

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