How to select or filter SNPs or selecting Tag SNPs based on physical position, LD and PIC value in R?

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4.7 years ago

blacktomato27 ▴ 70

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.

R SNP snp genome • 977 views

ADD COMMENT • link updated 4.7 years ago by zx8754 12k • written 4.7 years ago by blacktomato27 ▴ 70

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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.

ADD REPLY • link 4.7 years ago by zx8754 12k

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