[R] return counts of elements on a table column depending on elements on another column

[Martin Morgan]

On 06/08/2011 03:06 PM, ads pit wrote:
> Hi,
> I am given the following table:
>> head(hsa_refseq)
>     chr       genome region    start     stop nu strand nu.1    nu.2
> gene_id
> 1 chr1 hg19_refGene    CDS 67000042 67000051  0      +    0 gene_id
> NM_032291
> 2 chr1 hg19_refGene   exon 66999825 67000051  0      +    . gene_id
> NM_032291
> 3 chr1 hg19_refGene    CDS 67091530 67091593  0      +    2 gene_id
> NM_032291
> 4 chr1 hg19_refGene   exon 67091530 67091593  0      +    . gene_id
> NM_032291
> 5 chr1 hg19_refGene    CDS 67098753 67098777  0      +    1 gene_id
> NM_032291
> 6 chr2 hg19_refGene   exon 67098753 67098777  0      +    . gene_id
> NM_032291
>
> What I've done is to find out how many of the elements on 3rd column are
> "CDS", "exon".
> sum(hsa_refseq$region=="CDS")
> sum(hsa_refseq$region=="exon")
>
>   But what I would like is to print for each chromosome how many are exons
> and how many CDS. For example
> chr1  has 5 CDS and 2 exons
> chr2  has 10 CDS and 3 exons...
>
> Can you tell what should I add? Or if I am doing this wrong, how should I do
> it?

Hi Nanami --

xtabs(~chr + region, hsa_refseq)

might do the ticket.

Martin

>
> Thank you,
> Regards,
> Nanami
>
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>
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