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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Will the arrow files being subset running subsetArchRProject() with dropCells = TRUE? #2087

Open qdong2023 opened 9 months ago

qdong2023 commented 9 months ago

Hi ArchR developers,

I was trying to subset the archr project for a few samples after QC using subsetArchRProject() and setting dropCells = TRUE. These samples were successfully removed from the subset archr project, however, their corresponding arrow files still exist in the new subset folder. It seems like the arrow files are not subset but only the archr project is. Besides subsetting by samples, I also need to subset by clusters, so copying full-size arrow files will take up too much space. Is it possible to subset arrow files while running subsetArchRProject()? Thanks!

I am using devtools::install_github("GreenleafLab/ArchR", ref="dev", repos = BiocManager::repositories()). v'1.0.3'.

rcorces commented 9 months ago

Hi @qdong2023! 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.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help. Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response.
In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Did you post your log file? If not, add it now. 3.__ Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.