refactoring code

[jkanche]

This is based on a prior discussion, mostly moving things around:

• create atac sce from fragment list
• create gene-level sce from fragment list (e.g. like GeneAccessibilityMatrix)
• combine sce's to MAE
• create a utils.R

This moves the current functions around, probably doesn't work :)

[xiaosaiyao]

I further consolidated the ATAC functions under createATACSCE.R. I reserved utils.R for file clean up functions