Hi, Ruppert.

You might want to look at the XML package for doing such things.

Sean


On Mon, Mar 14, 2011 at 4:18 PM, Ruppert Valentino <ruppert7@hotmail.com>wrote:

>
>
> Hello,
>
> I am trying to write a script that will enter miRNA and get the predicted
> target genes for that miRNA. I am trying to use various software to do this,
> one of them is TargetScan. The problem is that I don't know how to parse the
> HTML output table so that I can get the target genes only.
>
> For example I am search for target genes for the miRNA mmu-miR-1 as
> follows:
>
>
> http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&gid=&mir_sc=&mir_c=&mir_nc=&mirg=mmu-miR-1
>
> This generates a table
>
>
>
> The script is:
>
> URL <- "
> http://www.targetscan.org/cgi-bin/targetscan/vert_50/targetscan.cgi?species=Human&gid=&mir_sc=&mir_c=&mir_nc=&mirg=mmu-miR-1
> "
> dat <- readLines(URL)
>
>
> But I don't know how to parse the table to separate it into columns then I
> can take the column entitled "Human ortholog of target gene" which would
> have the target genes.
>
>
> In the example above the first gene COL4A3 starts at HTML code:
>
> <td><a href="
> http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=1285"
> target=new>COL4A3
>
>
>
> Is there any way to format such a table into columns then transpose the
> column entitled "Human ortholog of target gene" and pass that to a variable?
>
>
> Many thanks,
>
>
>
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