Hi, I am trying to help a labmate who is using DiffBind to do a PCA analysis on some ATAC-seq data that she generated. I have experience with PCA but not with this specific software. How can we retrieve the PCA loadings/eigenvalues for each individual for each PC? I am used to using other PCA tools that allow you to retried the spreadsheet of loadings/eigenvalues in addition to plotting PC's 1-10 against each other. As far as I can tell DiffBind allows you to plot PC1, PC2, and PC3 against each other but does not provide the actual numbers, nor does it provide access to any further PC's. Any help with this would be greatly appreciated.
DiffBind does allow any components to be plotted again any other components by specifying which components to plot using components= when calling dba.plotPCA() (the default is components=1:3 but this may be changed by the user).
There is no way to directly retrieve the computed PCA data. You can retrieve the underlying read count data (normalized by default) using dba.peakset() with bRetrieve=TRUE and run a PCA on that.