New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Loading 10x Genomics Data: Error in step_subset #214
Comments
Hi, @mdozmorov! We have managed to reproduce your issue. Now we are working on fixing it. I will get back to you with any updates. Thank you so much for drawing our attention to this. Good luck, |
Hello, @mdozmorov |
Thanks, Maria, I followed your instructions verbatim, but the problem still persists. I did reinstall immunarch from the dev branch, updated all packages, ensured global and local workspace restoring is disabled. I'm copy-pasting the code, the error is identical. # 1.1) Load the package into R:
# devtools::install_github("immunomind/immunarch", ref="dev")
library(immunarch)
# 1.2) Replace with the path to your processed 10x data or to the clonotypes file
file_path = "/Users/mdozmorov/Documents/Data/VCU_work/test_immunarch/data"
# 1.3) Load 10x data with repLoad
immdata_10x <- repLoad(file_path) |
Hi, @mdozmorov! My name is Aleksandr Popov, I am a developer of the Immunarch package. When I tried to reproduce this bug, I noticed that it appears only when there are remains of old version of Immunarch, or there are function name conflicts in R environment. Please try to run R from terminal with
I hope this will help to load the data correctly. Best regards, |
It didn't help. The
Manually removing it rm -r /Users/mdozmorov/Library/R/x86_64/4.1/library/immunarch and reinstalling still results in the same error. |
Hello, @mdozmorov! I suppose that error persits as you try to load all files from your folder in Immunarch. But Immunarch could load only files with proper format. Please try to replace the
Do not hesitate to contact us with any questions further along. Good luck, |
Hello, I get the same error when loading my 10x genomics results. I installed your dev version package and restart my Rstudio and get same error. my error is like this: == Step 1/3: loading repertoire files... == Processing "" ... #version session info Matrix products: default locale: attached base packages: other attached packages: loaded via a namespace (and not attached): Then I tested several versions of the package and only versions before 0.6.5 can load 10x data correctly. That means 0.6.4 can load 10x genomics data, but 0.6.5 0.6.7 not. Hope you can give me some suggestions. Thank you! |
Hi, @shanshenbing! Thank you for contacting us. I suppose that error persits as package versions conflict in Rstudio. To test it, write on the command line:
Than install proper version of immunarch again and repeat your command (on the command line too). If everything will be ok, just update Rstudio projects, otherwise let us know. Do not hesitate to contact us with any questions further along. Good luck, |
Hello. I started with the Loading 10x Genomics Data tutorial, downloaded the CSV files from 10X website and ran
immdata_10x <- repLoad(file_path)
. It results in error, reproducible with the data I actually want to analyze:The files I downloaded and put in a separate
file_path
folder are:I'm using Immunarch v.0.6.7 on a Mac. What may be wrong?
The text was updated successfully, but these errors were encountered: