PCA Analysis Methods

Data from single cell object v3.3 were used for this analysis. For code associated with this analysis, visit the PCA Explorer repository on the PanKbase Github.

Obtaining per-donor counts per million (CPM) matrices:

1. Using the single cell object v3.3, raw counts were summed on a per-gene, per-donor basis.
2. Counts were then normalized per-donor using CPM.

PCA analysis:

1. PCA analysis was performed using the prcomp function in R with scale = TRUE.
2. PCA results were merged with donor-level metadata to create plots in the PCA Explorer.