Hi:
Here are a couple of ways to render a basic 2D table. Let's call your input
data frame dat:
> names(dat) <- c('samp', 'sequen')
> ssTab <- as.data.frame(with(dat, table(samp, sequen)))
> ssTab # data frame version
samp sequen Freq
1 111 abc 1
2 1079 abc 1
3 5576 abc 1
4 111 sdf 1
5 1079 sdf 0
6 5576 sdf 2
7 111 xyz 1
8 1079 xyz 2
9 5576 xyz 0
> with(dat, table(samp, sequen)) # table version
sequen
samp abc sdf xyz
111 1 1 1
1079 1 0 2
5576 1 2 0
HTH,
Dennis
On Wed, Aug 25, 2010 at 7:53 AM, rtsweeney <tripswee...@gmail.com> wrote:
>
> Hi all,
> I have read posts of heat map creation but I am one step prior --
> Here is what I am trying to do and wonder if you have any tips?
> We are trying to map sequence reads from tumors to viral genomes.
>
> Example input file :
> 111 abc
> 111 sdf
> 111 xyz
> 1079 abc
> 1079 xyz
> 1079 xyz
> 5576 abc
> 5576 sdf
> 5576 sdf
>
> How may xyz's are there for 1079 and 111? How many abc's, etc?
> How many times did reads from sample (1079) align to virus xyz.
> In some cases there are thousands per virus in a give sample, sometimes
> one.
> The original file (two columns by tens of thousands of rows; 20 MB) is
> text file (tab delimited).
>
> Output file:
> abc sdf xyz
> 111 1 1 1
> 1079 1 0 2
> 5576 1 2 0
>
> Or, other ways to generate this data so I can then use it for heat map
> creation?
>
> Thanks for any help you may have,
>
> rtsweeney
> palo alto, ca
> --
> View this message in context:
> http://r.789695.n4.nabble.com/frequency-count-rows-data-for-heat-map-tp2338363p2338363.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
