[R] frequency, count rows, data for heat map

rtsweeney tripsweeney at gmail.com
Wed Aug 25 16:53:38 CEST 2010

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

Thanks for any help you may have, 

palo alto, ca
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