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May 30, 2023, 10:00:14 AM5/30/23
to poppr

I encountered the following error while executing the DAPC script. May I ask how to solve this big data file processing? My file is a 12Gb SNP file. When I use Rstudio, "Error: cannot allocate vector of size 24.6 Gb" is displayed in "read. vcfR". When using Linux R, "NA overflow" is displayed in "x", and "grp<- find. clusters (x, max. n. cluster=40)" is running continuously. Additionally, Can the DAPC script display the proportion of PC1 and PC2, and how to implement it? Thank you. 

Xu Jun

Zhian Kamvar

May 30, 2023, 1:11:24 PM5/30/23
to 林子熙, poppr
Unfortunately, it sounds like you do not have enough memory on your computer to process this file in R (which needs 2x the amount of memory for the size of the file). I would suggest filtering your snps for quality and missingness before passing into R.

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May 31, 2023, 1:09:40 AM5/31/23
to poppr
Hi, is there any packages or software you know that can do the same thing as DAPC for huge data ?Whether to do PCA analysis alone should not be very persuasive?
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