Have you looked here (found immediately by an internet search!)? https://cran.r-project.org/web/packages/LDheatmap/vignettes/LDheatmap.pdf
Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Feb 3, 2016 at 1:49 PM, Ashta <sewa...@gmail.com> wrote: > Hi all, > > I am looking for an R package that calculates a pair wise LD > (linkage disequilibrium) I came up with library(LDheatmap). has any > one used this library? I would appreciate if I get a help how to use > this library for my set of data.. > > > My data set look like > > Geno file > Name1 1 1 2 2 2 2 > Name2 2 2 2 2 2 2 > Name3 2 2 2 2 2 2 > Name4 2 2 2 2 2 2 > Name5 1 1 2 2 2 2 > > > NameN 1 1 1 2 2 2 2 > > > The other file is map file > Chromosome, SNP, Location (physical) > > > Thank you in advance > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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 -- To UNSUBSCRIBE and more, see 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.
