Releases: TARGENE/ld-block-removal
Releases · TARGENE/ld-block-removal
v0.1.0
This release has added functionality such that it performs PCA on genotyped SNPs, removing all SNPs contained in LD blocks. It first computes the regions of LD around SNPs-of-interest, removes those regions from downstream analysis, performs LD pruning via plink2, MAD thresholding and finally PCA on the remaining SNPs. Final output is a Scree Plot showing the proportion of variance explained across the PCs.