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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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predictionCutoff parameter in addPeak2GeneLinks #1832

Open rcorces opened 1 year ago

rcorces commented 1 year ago

Discussed in https://github.com/GreenleafLab/ArchR/discussions/1814

Originally posted by **RegnerM2015** January 19, 2023 Hi @rcorces and @jeffmgranja , I was looking at the source code for `addPeak2GeneLinks` and the use of predictionCutoff: https://github.com/GreenleafLab/ArchR/blob/f6c0388bd37023400794c9ae8562ad69e3ba9fd7/R/IntegrativeAnalysis.R#L1035-L1057 It appears that the predictionCutoff is used to subset `dfAll` but is not used later on when making metacells. The object `dfAll` is also not used later on. If I am misinterpreting, if you could point me in the direction of where predictionCutoff is used to subset out cells, that would be greatly appreciated! Thank you for your help.
rcorces commented 1 year ago

Hi @rcorces! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
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