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-- Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." Clifford Stoll On Sat, Aug 2, 2014 at 11:47 AM, Don McKenzie <d...@u.washington.edu> wrote: > David’s answer assumes a more complicated objective, but obviously we are > both unclear as to what you want. Are you trying to find out which clusters > have a unique pattern of mutation? (probably all of them, with so few > clusters and so many genes?) > > For either objective, this is not a statistical test, but a problem of > identification. For the simpler question, create a data frame with each row > being the 150 1s and 0s associated with each cluster, and use duplicated() to > identify unique rows. (unique rows will return “FALSE”) > > Untested > > On Aug 2, 2014, at 11:41 AM, David Winsemius <dwinsem...@comcast.net> wrote: > >> >> 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 >>> >>> [[alternative HTML version deleted]] >> >> This is a plain text mailing list. >> >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >> >> David Winsemius >> Alameda, CA, USA >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > Don McKenzie > Research Ecologist > Pacific Wildland Fire Sciences Lab > US Forest Service > > Affiliate Professor > School of Environmental and Forest Sciences > University of Washington > d...@uw.edu > > > > > > [[alternative HTML version deleted]] > > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
