search

GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
384 stars 137 forks source link

Not Valid Collection in ArchRAnno Database #516

Closed jindalk closed 3 years ago

jindalk commented 3 years ago

ArchR-addArchRAnnotations-c8613ddc2be3-Date-2021-01-27_Time-13-01-57.log

I tried to add ATAC peak collection to my mm10 project using:

proj_lsk4 <- addArchRAnnotations2(ArchRProj = proj_lsk4, db = "LOLA", collection = "ATAC")

and got the following error:

Not Valid Collection in ArchRAnno Database!

However, this works fine with EncodeTFBS

rcorces commented 3 years ago

In the future, please make sure to use the issue templates provided. This information is pretty explicit in the function parameter documentation and you might have found this if following the issue template. The error is also quite explicit. https://www.archrproject.com/reference/addArchRAnnotations.html

collection A string indicating which collection within the database to collect for annotation. For ArchR, options are "ATAC", "EncodeTFBS", "CistromeTFBS", or "Codex". For LOLA, options include "EncodeTFBS" "CistromeTFBS", "CistromeEpigenome", "Codex", or "SheffieldDnase". If supplying a custom ArchRAnno file please select a valid collection from within that database.