Re: [R] How to make this binary hit matrix

From: ssls sddd <ssls.sddd_at_gmail.com>
Date: Sun, 15 Jun 2008 14:06:00 -0400

Thank you very much, Marc!

Have a great weekend!

Alex

On Sun, Jun 15, 2008 at 1:58 PM, Marc Schwartz <marc_schwartz_at_comcast.net> wrote:

> on 06/15/2008 12:46 PM ssls sddd wrote:
>
>> Hi all,
>>
>> Basically I want to make a binary hit matrix.
>>
>> For instance, if I have a file called 'pair.txt':
>>
>> set_a gene_1
>> set_a gene_2
>> set_a gene_3
>> set_b gene_3
>> set_b gene_4
>> set_b gene_5
>> set_c gene_1
>> set_c gene_3
>>
>> And I want to convert it to a binary matrix as:
>>
>> Rows set_a set_b set_c
>> gene_1 1 0 1
>> gene_2 1 0 0
>> gene_3 1 1 1
>> gene_4 0 1 0
>> gene_5 0 1 0
>>
>> Can anyone suggest how to do this?
>>
>> Thank you!
>>
>> Alex
>>
>
> Presuming that your data is contained in a data frame called 'DF':
>
> > DF
> V1 V2
> 1 set_a gene_1
> 2 set_a gene_2
> 3 set_a gene_3
> 4 set_b gene_3
> 5 set_b gene_4
> 6 set_b gene_5
> 7 set_c gene_1
> 8 set_c gene_3
>
>
> You can use:
>
> > t(table(DF))
> V1
> V2 set_a set_b set_c
> gene_1 1 0 1
> gene_2 1 0 0
> gene_3 1 1 1
> gene_4 0 1 0
> gene_5 0 1 0
>
>
> See ?table and ?t
>
> HTH,
>
> Marc Schwartz
>

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