[R] mutually exclusive events
john.archie.mckown at gmail.com
Sat Aug 2 22:19:43 CEST 2014
On Sat, Aug 2, 2014 at 1:11 PM, Adrian Johnson
<oriolebaltimore at gmail.com> wrote:
> I am trying to identify mutually exclusive events from the following
> 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
> Thanks a lot.
I am having trouble visualizing your data. How about a sample? The
easy is to do something like:
temp <- head(realData,10);
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. As an aside any value other than 0, 1, 2,4, or 8 could be
considered invalid because it means that more than one column is TRUE,
which violates your constraint.
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