Re-coding genotype in JMPG yields incomplete output dataset
Jul 6, 2018 8:11 AM(499 views)
I am trying to re-code a genotype data set (~ 40 k SNPs) from diploid format (eg A / G, G / C, etc) to numerical format (0, homo; 1, hete; 2, homo). The re-coding looks good, the issue is that my data output Is incomplete (it only contains ~ 29 k SNPs). I am not getting any error or massage indicating what happened with the rest of my markers.
Could you please give me any clue to solve this issue
That is currious. I just recoded 295988 SNPs from AA, AB, and BB to 0,1, and 2. All of the SNPs are there. I am using JMP Genomics 9.0.
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Chris Kirchberg Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement SAS Institute, Inc. - Denver, CO Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: firstname.lastname@example.org JMP – A Division of SAS Institute | www.jmp.com