On Aug 2, 2014, at 11:11 AM, Adrian Johnson wrote:
> Hi:
>
> I am trying to identify mutually exclusive events from the following
> example:
>
#-------------
dat <- read.table(text="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", header=TRUE,
stringsAsFactors=FALSE)
with(dat, table(Cluster, Gene, Mutated) )
#----------------
, , Mutated = 0
Gene
Cluster G1 G2 G3 G4 G5
1 0 0 1 1 0
2 1 0 0 1 0
, , Mutated = 1
Gene
Cluster G1 G2 G3 G4 G5
1 1 1 0 0 1
2 0 1 1 0 1
#--------------
Or:
xtabs(Mutated ~ Cluster+Gene, data=dat)
#----------------
Gene
Cluster G1 G2 G3 G4 G5
1 1 1 0 0 1
2 0 1 1 0 1
I'm a bit unclear about your goals. Are you trying to identify the "Gene"s that
have only one "Cluster" mutated as the "G1-G3" events and the Gene's that have
either-Cluster but not both as the "G2-G5" events?
If so you can choose the columns that have a sum of 2 for the first and columns
with sum of 1 for the second.
>
>
> 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.
It's even less clear what sort of "test" you propose. `fisher.test` is a test
of association. It doesn't identify combinations.
>
> Thanks a lot.
>
> -Adrian
>
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David Winsemius
Alameda, CA, USA
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