On Tue, 6 Jan 2009, Sake wrote:
Hi,
I'm heaving difficulties with a dataset containing gene names and positions
of those genes.
Not such a big problem, but each gene has multiple exons so it's hard to say
where de gene starts and where it ends. I want the starting and ending
position of each gene in my dataset.
This looks like a minor variant on the 'first and last observation' thread
from a few days ago:
http://thread.gmane.org/gmane.comp.lang.r.general/135411
to which several useful solutions were posted.
I suggest you read that thread and try to adapt what is there to your
situation.
If this does not get you all the way there, when you post back it will
help to "provide commented, minimal, self-contained, reproducible code".
What you have given us is not quite there.
Here is a start:
data <-
read.csv("http://www.nabble.com/file/p21312449/genlistchrompos.csv",sep=';')
and note that
colnames(data)
[1] "Query" "Gene" "Chrom" "Strand"
"Accession"
[6] "Exon" "Exon_Start.Chr." "Exon_Stop.Chr." "Exon_Start.Trans."
"Exon_Stop.Trans."
does not include anything like "Column 'B'", so refer to those column
names if you need further help after studying the thread above.
HTH,
Chuck
Attached is the dataset:
http://www.nabble.com/file/p21312449/genlistchrompos.csv genlistchrompos.csv
Column 'B' is the gene name, 'G' is the starting position and 'H' is the
stop position.
You can load the dataset by using: data<-read.csv("genlistchrompos.csv",
sep=";")
I hope someone can help me, it's giving me headaches for a week now:-((.
Thanks!
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Charles C. Berry (858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
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