Option to output scores for all edges and regulators

[agitter]

GENIE3 is a popular network inference approach. It provides a way to output all regulator-target edges: https://github.com/aertslab/GENIE3/blob/master/vignettes/GENIE3.Rmd#L116

SINGE already has a similar output format but does not output edges with a score of 0. The 0s in the output are edges that had a non-zero score before rounding

SINGE/code/SCINGE.m

Line 38 in 8e75a50

ranked_edgesw.SCINGE_Score = floor(ranked_edgesw.SCINGE_Score*10^5)/10^5;

We could consider adding an optional parameter in the config file that would output all edge scores and all regulator scores even if they are 0. That would help users use SINGE in downstream analyses set up for GENIE3.