Assistance Required: Error with MuSiC2 Package - "pVar" Function Not Found

Question

[Pumla]

Dear BioStars Bioinformatics Team,

I hope you can assist me with an issue I'm encountering while using the MuSiC2 package in R.

When attempting to run the music2_prop function, I am receiving the following error:

javascript Error in pVar(x, clusters) : could not find function "pVar"

Despite ensuring that all necessary packages (such as Biobase and BiocGenerics) are properly installed and loaded, the issue persists.

Here is the code I am using:

R
est.prop <- music2_prop(
  bulk.eset = benchmark.eset, 
  sc.eset = seger.eset, 
  condition = 'group',      # The column in bulk.eset that defines condition (healthy/T2D)
  control = 'healthy',      # The reference condition (matches scRNA-seq dataset)
  case = 't2d',             # The condition being tested
  clusters = 'cellType',    # Column in scRNA-seq defining cell types
  samples = 'sampleID',     # Column in scRNA-seq defining sample IDs
  select.ct = c('acinar', 'alpha', 'beta', 'delta', 'ductal', 'gamma'),  # Select cell types
  n_resample = 20,          # Number of resamples for detecting DE genes
  sample_prop = 0.5,        # Fraction of samples used per resample
  cutoff_c = 0.05,          # Cutoff for common cell types
  cutoff_r = 0.01           # Cutoff for rare cell types
)

I have already tried reinstalling the package, but the error continues. I would appreciate it if you could guide me on how to resolve this issue or if there are additional steps I need to follow.

Thank you for your time and assistance.

Best regards,

[Bastien Hervé]

https://github.com/xuranw/MuSiC/issues/3

Try :

library(xbioc)