“object ‘..sample_identity’ not found ” error in permutation_test with scProportionTest

Hi everyone,

I’m new here and I’m also quite new in the world of scRNA seq analysis so I apologize for the mistakes in format I will probably make.

I am analyzing some scRNA seq data, I have a dataset with 2 control animals and 2 mutants. I want to analyze if there is a significant difference in the proportion of cells between these two groups. I found a post correct way of analyzing cell proportions in singlecell data where rpolicastro presents a very useful R library he created. However, I tried to use it but I get this error and I don’t know what else to try:

Error in `[.data.frame`(meta.data, get(sample_identity) %in% c(sample_1,  : object '..sample_identity' not found 

And this is the traceback:

3.`[.data.frame`(meta.data, get(sample_identity) %in% c(sample_1, 
sample_2), c(..sample_identity, ..cluster_identity)) 

2.meta.data[get(sample_identity) %in% c(sample_1, sample_2), c(..sample_identity, 
..cluster_identity)] 

1. permutation_test(clustered.by.ref, cluster_identity = active.ident, 
sample_1 = starts_with("C"), sample_2 = starts_with("k")) 

sample_identity is one of the arguments of the function so I don’t understand why R cannot find it.

Thank you for your help!