Hi r-help-boun...@r-project.org napsal dne 13.06.2011 17:59:03:
> Ben Ganzfried <ben.ganzfr...@gmail.com> > Odeslal: r-help-boun...@r-project.org > > 13.06.2011 17:59 > > Komu > > r-help@r-project.org > > Kopie > > Předmět > > [R] log2() and -min() very quick question > > I'm looking over good-code a post-doc in my lab wrote and trying to learn > how it works. I came across the following: > rel.abundance <- as.matrix(read.delim("rel.abundance.csv",row.names=1,as.is > =TRUE)) > rel.abundance <- log2(rel.abundance-min(rel.abundance)+1) > > I'm not sure what the second line is doing. I ran each line in R and > couldn't see a noticeable difference in the output. I assume log2() takes > the log base 2 of the values? I'm not clear what -min(rel.abundance) is > doing either...my hunch would be that it would take the smallest value in > each row? No. If rel.abundance is matrix min(rel.abundance) is overall minimum > mat<-matrix(1:12, 3,4) > min(mat) [1] 1 so log2(rel.abundance-min(rel.abundance)+1) subtract minimum value from all numbers, after that it add 1 do all numbers, takes log base 2 from each number and returns matrix with the same dimensions as input matrix. > I'd really like to figure out: > 1) What's actually going on? > 2) Is there a good way to run a command over a large dataset in R and better > be able to tell what is going on? More specifically, when I run each line > in R it looks something like this (w/ dif. values per row): > Archaea|Euryarchaeota|Methanobacteria|Methanobacteriales| > Methanobacteriaceae|Methanobrevibacter,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,3,0,0,0,0,0, > 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, > 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2, > 0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,23,0,3,0,0,0 > > > There are a lot of cells w/ values per row, which is one reason why I think > it is difficult to detect a pattern.... there are some summary and structure commands summary(data) or str(data) which can tell you some overall information about your data. Regards Petr > > Thanks in advance! > > Ben > > [[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.