I'm using package
HiTC_1.22.1) to find A/B compartments in my data.
I tried to use
gene.gr parameter to directly link eigenvector sign with A/B annotation. However, I got very different results from the ones obtained when trying to compute gene density myself.
pca.hic function, it seems that gene density is actually gene number per sign, whatever the number of bins is.
Is there a bug in
pca.hic function (like function
sum is used instead of
mean - lines 47 and 48
https://github.com/nservant/HiTC/blob/master/R/pca.R) or am I missing something?