How to handle 30000 SNPs genotyping data of 500 individuals in R?
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5.8 years ago

Dear All Good Morning

I have 30000 SNP genotyping data on 500 individuals and it is quite big data for me (approx. 80mb size) and i have only 4GB RAM and 1TG HDD. My final objective to diversity analysis and grouping these individuals based on their similarity. I tried to calculate genetic distance in R using POPPR package but i am getting memory insufficient error and i tried to convert my data to Genlight Object but no success. Are there any package in R to handle this size of data? Here i am requesting you to share your expertise and suggestion to solve this this. Any help in this regard is highly appreciated. This is my example data file :https://www.dropbox.com/s/phq1szmqlttsdja/test.txt?dl=0 Thanks in Advance Regards

R SNP • 1.5k views
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Yes, the resulting distance matrix would be enormous. What are the exact commands and error messages that you're using and receiving? There are ways of increasing memory in R but there is always going to be a limit somewhere along the line. Will pick this up in the morning (night here).

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Dear kevin good morning thank you very much for your reply. I using Poppr package to calculate genetic distance. i am not getting any error from code but getting error like "can not allocate 24.5GB data". Thanking you

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Then, it is trying to allocate 24.5GB of RAM. Most likely, your computer does not have that. Do you have access to a super-compute cluster?

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Dear Kevin unfortunately no thanks for your reply

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Please paste the exact command that you're using. Perhaps I can modify the code such that it could work.

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Dear Kevin Good Afternoon sorry for my late reply and i am using following code to calculate GD please find my small code here https://www.dropbox.com/s/6wlftpd253fw2x3/code.txt?dl=0 and here is my example data https://www.dropbox.com/s/jw509iylda59xfv/example%20data.csv?dl=0 With this limitation i am even not able to do DAPC (descriminative analysis pf principle component) to identify groups, i mean how these individuals are grouped based on their relatedness Thanking you very much for your help Regards

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