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 <tripsweeney@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.
>
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> PLEASE do read the posting guide
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>

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