cahanlab / epoch Goto Github PK

Hi,
I'm interested in using epoch on data processed in R with Seurat. As I'll be extracting the data from the Seurat object rather than a loom file, I was wondering if you could provide a brief definition of the data that should be in the objects you save in variables expDat and sampTab?

From a quick look at the code I think sampTab should be cell metadata and expDat should be a genes x cells matrix of (normalised & log-transformed) expression data, is that correct? It would be really helpful if this info was included in the example analysis to make it easier to follow.

Thanks!

During the findDynGenes step, if I only select a subset of groups as path. It's highly likely to get the "subscript out of bounds" error during the expSmooth[genes, ] step. The reason why this happens is that the sum of gene expression in certain genes may become NA due to that the gene only expresses in those group that I didn't choose. The suggested solution for this error is to eliminate those genes that sum in the selected groups is 0.

Hi,
I am unfortunately unable to install the package. I receive the following error when trying:

ERROR: unable to collate and parse R files for package ‘epoch’

Any suggestion what the cause for this might be and/or how to fix it? Thank you.