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Single Cell Proportion Test
In order to identify differences in proportions of cell types between conditions, scProportionTest can be run. It reads in a seurat object and runs a permutation test to calculate a p-value for each cluster and a magnitude difference between conditions. It also generates a plot showing the pvalues and difference. It can be used to identify enriched or depleted cell types between conditions.
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library("scProportionTest")
#read in seurat object, saved as a RData file
load("seurat.RData")
#read in seurat object (pbmc), assuming that pbmc has multiple samples with different condition identities
prop_test <- sc_utils(pbmc) |
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#run permutation test to compare between cells with orig.ident as 'Con' and ident 'Treatment'
#run it for every cluster
prop_test <- permutation_test(
prop_test, cluster_identity = "custom_clusters",
sample_1 = "Con", sample_2 = "Treatment",
sample_identity = "orig.ident"
) |
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#Generate plot
permutation_plot(prop_test) |
| View file |
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| name | permutation_plot.l2.pdf |
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