On Sat, Aug 2, 2014 at 1:11 PM, Adrian Johnson <oriolebaltimore@gmail.com>
wrote:
> Hi:
>
> I am trying to identify mutually exclusive events from the following
> example:
>
>
> Cluster Gene Mutated not-mutated
> 1 G1 1 0
> 1 G2 1 0
> 1 G3 0 1
> 1 G4 0 1
> 1 G5 1 0
> 2 G1 0 1
> 2 G2 1 0
> 2 G3 1 0
> 2 G4 0 0
> 2 G5 1 0
>
>
> In cluster 1 : G1, G2, G5 are mutated
>
> In cluster 2: G2, G3, G5 are mutated.
>
>
> I am interested in finding such G2-G5 event and G1-G3 events.
>
> In total I have a 8 clusters and 150 gene (1200 rows x 4 columns).
>
> What test could be appropriate to identify such pairs.
>
> In my naive understanding would a fishers-exact test give such
> combinations.
>
> Thanks a lot.
>
> -Adrian

I am having trouble visualizing your data. How about a sample? The easy is
to do something like:

temp <- head(realData,10);
dput(temp);

Then cut'n'paste the output from the dput() into another email here.

But, asuming I have a bit of a grasp, you have four columns (example only
shows 3). If you have a set of columns which are 0 & 1 or FALSE and TRUE,
then you can create a "temp" column which encodes tehm simply by
considering them to be binary digits in a number. I.e. tempColumn = 1 *
column1 + 2 * column2 + 4*column3 + 8*column4. You can the "group" the data
by this value. All rows with the same value are in the same "group". But I
don't know what you want your output to look like.

--
There is nothing more pleasant than traveling and meeting new people!
Genghis Khan

Maranatha! <><
John McKown

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