cnobles / gintools Goto Github PK

Add a delimiter option to make the function appropriate for other formats.

For integration site analysis, standardizing integration site positions makes complete sense, but for oligo incorporation, it does not. This is because oligo incorporation may appear downstream of the actual double strand break, and therefore is similar to a break point induced by sonication.

Changing the function to resolve_edges or something and including an option for target = [lead, lag, both] might work well.

Absorb dualDemultiplexR, seqTrimR, seqFiltR, seqConsolidateR, and blatCoupleR code into gintools.

This should help with reducing code duplication and increase modularity, though the package will get quite large compared to it's current size. This will also mean that analytical functions such as standardize sites and refine_breakpoints, as well as others, will be available in the environment.

This error occurred for me in the CHIVA pipeline. Specifically on the line:
sites.to.condense$group.id <- paste0(group, "^", sites.to.condense$posid)
Error in [[<-(*tmp*, name, value = "^") :
1 elements in value to replace 0 elements

Both standardize_intsites() and refine_breakpoints() will add some columns at the end of processing containing summary data. I could make this add onto the data if requested by user, which could cleanup the data management quite a bit.