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I am trying to import three really big files (each file size >100GB) to R Studio but it complains of memory. I am using this version:
I tried increasing the memory limit by using (.Renviron) on terminal but it gives the same error.
How much actual memory does your mac have? There is no substitute for not having enough RAM unfortunately.
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My Mac has 16 GB memory.
I don't think this is going to work as is.
Edit: @zx5784's solution of using virtual memory on disk may work. With such large data set you may need to have patience in equally large amounts.
What kind of data is this? Alternatives:
- HPC with tonnes of memory
- Load data in chunks, do stuff, save results, load another chunk etc.
- Use packages that uses hard drive as memory and 'pretend' to have it as full object in R, e.g.: 'bigmemory' package.
Rstudio Mac Os X 10.9.5
See CRAN TaskView for HPC: Large memory and out-of-memory data
These are vcf files.
Do you need all the data at once, maybe slim it down first: filter on Samples, on Variants, or split on Chromosomes, etc. See bcftools for manipulating VCFs.
What operation are you trying to do with them? Perhaps there are command line alternatives that can be used instead of R. Are these files compressed or not?
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I am trying to use them for Upset R plot and these are not compressed.
Rstudio For Mac Os X 10.10.5
Rstudio For Mac Os X El Capitan
Is it to show overlapping Variants or Samples? Again you can get that info using bcftools, then file will be manageable for R.