Useful info


1. Comparing PCA and MCA


My code for PCA and MCA in earlier summaries was slightly off (only looking at 14 cell types). I’ve corrected this to look at all 19 cell types.


PCA

The loadings plots below show the coefficient of the linear combination of variables making up each dimension. PC1 compares quiescent and heterochromatin (high) with transcribed and enhancer (low) regions, whereby SNPs lying in a quiescent region in CD3 peripheral cells will be given a large value and those in transcribed regions in CD56 cells will be given a small value when mapped ono this first dimension.

Interestingly, PC2 compares transribed wiht enhancer regions.