large SNP datasets in RDA analysis

[tonitsk-8264]

Dear Developer,

I have genome-wide SNP data for plants, but the number of loci is too large for my computational resources, and I cannot run RDA analysis successfully.

I am considering two options:

1. Perform LD pruning to reduce the number of SNPs.
2. Split the data by chromosome and run RDA on each separately.

Could you advise on the reliability of these approaches, or suggest a better alternative if you have one?

Best regards,

Tang

[gavinsimpson]

The bug reports section for vgean is not a good place to ask these questions, especially as you question isnt about vegan, per se.

[jarioksa]

I just started to look at running RDA etc with big data. In which way you cannot run RDA successfully? What is the error message or the problem? How does the analysis fail?

Can you run RDA using the new CRAN package fastrda?