In silico CHIP chromVAR scores are not returning most TFs

[Connorr0]

After running the pipeline I noticed that while the FIMO matrix returns ~1,000 TFs and the gene-TF links return ~800 TFs, the In silico CHIP chromVAR scores are only calculated for ~200 TFs.

[jordanc17]

You can adjust the parameters used to perform filtering in config. yaml. The default is requiring 30 peaks with an in silico ChIP score > .15 for a TF to pass filtering:

ins_chip:
    # set verbose to "--verbose" for True
    verbose: ""
    min_chip_score: 0.15
    min_peak_hits: 30

The NAs in the chromVAR deviations occur when the expected number of fragments in the cell is less than 1, according to GreenleafLab/chromVAR/issues/27. I've been filling the NA values with the minimum chromVAR score for that TF. Signac fills the missing values with zeros as seen in stuart-lab/signac/issues/1254. Missing values need to be filled in run_chromvar.R before export.