Filename for unfiltered TF-peak-gene GRN and default filter for r_peak_gene
Upon reinspecting the code, I realized two things and wanted to mention this here, this is relevant for @akamal :
- The file GRN_withGenes_TF-PeakFDR0.3_peakGene_rawP0.3.tsv.gz suggests the peakGene threshold used was rawP = 0.3, while this is actually FDR 0.3, The correct name should be, and is now, GRN_withGenes_TF-PeakFDR0.3_peakGeneFDR0.3.tsv.gz. The content of the file was correct, just the filename was not - sorry.
- Also, this is I think what @akamal mentioned once (to me and Judith), it contains an unfiltered version of the peak-gene connections. That is, both positive and negative peak-gene pairs. In all other cases when calling the filter function, I did use the restriction of only keeping r > 0 peak-gene pairs, but for this "unfiltered" object, it was not the case. I did that deliberately but didn't make it clear enough I think or forgot this detail. Sorry again! But I guess you figured that out already and filtered the r < 0 peak-gene pairs. I changed it and no also restrict it to the positive r peak-gene pairs.
Please close when you read it and when the implications are clear.
Edited by Christian Arnold