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 Жыл бұрын
Could you make a video showing how you generated the snp data inform of 1 and 0
@HaileG-202010 ай бұрын
Dear Sir, I have VCF file format, how to arrange the file for PCA, structure analysis based on your analysis?
@tamaram4444 жыл бұрын
Can you show how you input your SNP matrix in the first part?
@tamaram4444 жыл бұрын
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-ht6le5 жыл бұрын
your input data contains columns for genotypes and rows for markers?
@KevinFalk5 жыл бұрын
Rows for genotypes and columns for markers
@KevinFalk5 жыл бұрын
Each column is a SNP molecular marker. Each row is a different genotype.
@boukailsameh31075 жыл бұрын
Hello, thanks for the video, do you have any video of the way to perform a 3D PCA? Thanks :)
@KevinFalk5 жыл бұрын
No, not in R. I have done 3D PCA before using JMP.
@KevinFalk5 жыл бұрын
Hi Boukail, I use JMP software to perform a 3D PCA. I'm sure you could probably also do it in R.
@mindlessgreen4 жыл бұрын
Hmmm.. Doesn't standard PCA assume normally distributed data? And if we have binary data, shouldn't we use logistic PCA or something?