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Roy-lab / scMTNI

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scATACseq_FBS.txt file missing #3

Closed pagarwal14 closed 1 year ago

pagarwal14 commented 2 years ago

Hi, I have installed the software and was trying to run the example but got an error in the first step about a missing file.

$ Rscript --vanilla Integration/LIGER_scRNAseq_scATAC_FBS.R Loading required package: cowplot

Note: As of version 1.0.0, cowplot does not change the default ggplot2 theme anymore. To recover the previous behavior, execute: theme_set(theme_cowplot())

Loading required package: Matrix Loading required package: patchwork

Attaching package: ‘patchwork’

The following object is masked from ‘package:cowplot’:

align_plots

[1] "Reading sample1" Error in fread(fname, header = T) : File 'scATACseq_FBS.txt' does not exist or is non-readable. getwd()=='/home/klp/installs/scMTNI' Execution halted

I looked around the downloaded code but could not find this file. Please let me know if it exists or if you need to add it to the repo.

Thanks Pankaj

shiluzhang commented 2 years ago

Hi Pankaj, Sorry for the late reply. I just added the missing files scATACseq.txt and scRNAseq.txt to ExampleData/ and updated the script in Scripts/Integration/LIGER_scRNAseq_scATAC.R. If you reclone the GitHub repository and reinstall it, it should work now. Please let me know if it still doesn't work.

Shilu