Re: [R] Re; Getting SNPS from PLINK to R

Resending to correct bad subject line... On Mon, 20 Jun 2011, Jim Silverton wrote: I a using plink on a large SNP dataset with a .map and .ped file. I want to get some sort of file say a list of all the SNPs that plink is saying that I have. ANyideas on how to do this? All the SNPs you hav

Re: [R] Re; Getting SNPS from PLINK to R

Hi Jim, If you convert the ped and map files to binary plink files the .bim file will tell you the name and the position of the snps. This would be the easiest method. Alternatively packages like GenABEL and genetics have functions to read in PLINK formatted data for analysis in R. Best wi

Re: [R] Re; Getting SNPS from PLINK to R

Hi Jim, If you convert the ped and map files to binary plink files the .bim file will tell you the name and the position of the snps. This would be the easiest method. Alternatively packages like GenABEL and genetics have functions to read in PLINK formatted data for analysis in R. Best wi

Re: [R] Re; Getting SNPS from PLINK to R

Hi, If you go to this site: http://pngu.mgh.harvard.edu/~purcell/plink/res.shtml#teach And download the teaching.zip file, I think there was information in the word document about reading plink data into R, though I am not 100% sure. I think a read.table("filename.ped", header=T) command may be e

[R] Re; Getting SNPS from PLINK to R

I a using plink on a large SNP dataset with a .map and .ped file. I want to get some sort of file say a list of all the SNPs that plink is saying that I have. ANyideas on how to do this? -- Thanks, Jim. [[alternative HTML version deleted]] __