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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