mutually exclusive events
On Sat, Aug 2, 2014 at 1:11 PM, Adrian Johnson
<oriolebaltimore at 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. 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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