Creating Principal Component Analysis PCA using SNP Genotypic data in R

[@HaileG-2020]

Dear Mighster, I sincerely appreciate the depth of insight provided in your KZbin tutorials. Would you be able to share an R script for performing LD pruning of SNP markers across varying thresholds (e.g., r²: 0.2, 0.4, 0.6, etc.) and for constructing LD decay curves for each population collectively? Your assistance would be immensely valuable.

[@SandraBabirye-t7d]

Could you make a video showing how you generated the snp data inform of 1 and 0

[@HaileG-2020]

Dear Sir, I have VCF file format, how to arrange the file for PCA, structure analysis based on your analysis?

[@tamaram444]

Can you show how you input your SNP matrix in the first part?

[@tamaram444]

Asking this because I'm loading SNP table in the way you've written to make a simple PCA with Adegenet, but the PCA plot is not loading. Any feedback would be helpful!

[@MN-ht6le]

your input data contains columns for genotypes and rows for markers?

[@KevinFalk]

Rows for genotypes and columns for markers

[@KevinFalk]

Each column is a SNP molecular marker. Each row is a different genotype.

[@boukailsameh3107]

Hello, thanks for the video, do you have any video of the way to perform a 3D PCA? Thanks :)

[@KevinFalk]

No, not in R. I have done 3D PCA before using JMP.

[@KevinFalk]

Hi Boukail, I use JMP software to perform a 3D PCA. I'm sure you could probably also do it in R.

[@mindlessgreen]

Hmmm.. Doesn't standard PCA assume normally distributed data? And if we have binary data, shouldn't we use logistic PCA or something?