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!
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