Hi to all,
I have 100K SNP genotyping data on 13 individuals with their physical positions, chromosome number, PIC and MAF values. Now i would like to select best up to 50 per chromosome on genome wide based on above criteria. I tried Hclust.R (http://www.compgen.pitt.edu/hclust/hclust.htm) but i am getting error like could not find function is.real and i am unable to do filter or to select best Tag snps. i need your help to select best snps in terms of procedure, packages or script in R or if any one provide to solve this error in Hclust.R will also be better for me.can any help help me in this regard
Thanks in advance.
That script is from 2005, since then R changed/updated many many times. Maybe explore other tools rather than trying to debug an old code?
I use prioritypruner for pruning based on additional info on top of LDs.