On Wed, Aug 29, 2012 at 10:16 AM, Stefan Dentro <sdentro@gmail.com> wrote:

> Hello,
>
> I'm trying to read in a VCF file containing mutation information from one
> sample, annotate it with Ensembl gene and GO information and then plot
> using ggbio. But I keep running into the problem of how to combine all
> information in one single GRange object.
>
> So I've got a VCF-class object and a data.frame containing for each
> mutation whether it is exonic, intronic or intergenic, a gene identifier
> (possibly NA) and a GO identifier (possibly NA).  ggbio accepts
> GRange-class objects so I would like to merge the VCF-class and data.frame
> into one GRange object containing all information.
>
> I can think of multiple ways of doing this, but none really work or are
> satisfactory:
> 1) read in the VCF, convert it into a GRange object. cbind elementMetadata
> with the data.frame and create a new GRange object.
>
> Problem: elementMetadata cannot be merged with a data.frame:
> Error in FUN(X[[3L]], ...) :
>   conversion of list columns to a data.frame is not supported
>
>
try a DataFrame instance



> 2) Directly annotate the VCF file through cbind, again:
> Error in FUN(X[[3L]], ...) :
>   conversion of list columns to a data.frame is not supported
>
> 3) Convert the VCF to GRange and add each column in the data.frame
> separately:
> gr$external_gene_id=df$external_gene_id
>
> There must be a simpler way to do this.
>
> 4) Convert the VCF into a tab delimited file using vcf-to-tab in vcftools
> and read it in as a data.frame. Merge both data.frames and create a GRange.
>
> I would think it is all possible within R, without converting the VCF-file
> first. This one comes really close though.
>
> It boils down to the following question: What is the proper way of doing
> this using the available R genomics packages?
>
> Best wishes,
> Stefan
>
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>
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