compare_lists {clustifyr} | R Documentation |
Calculate adjusted p-values for hypergeometric test of gene lists or jaccard index
compare_lists( bin_mat, marker_mat, n = 30000, metric = "hyper", output_high = TRUE, details_out = FALSE )
bin_mat |
binarized single-cell expression matrix, feed in by_cluster mat, if desired |
marker_mat |
matrix or dataframe of candidate genes for each cluster |
n |
number of genes in the genome |
metric |
adjusted p-value for hypergeometric test, or jaccard index |
output_high |
if true (by default to fit with rest of package), -log10 transform p-value |
details_out |
whether to also output shared gene list from jaccard |
matrix of numeric values, clusters from expr_mat as row names, cell types from marker_mat as column names
pbmc_mm <- matrixize_markers(pbmc_markers) pbmc_avg <- average_clusters( pbmc_matrix_small, pbmc_meta, cluster_col = "classified" ) pbmc_avgb <- binarize_expr(pbmc_avg) compare_lists( pbmc_avgb, pbmc_mm, metric = "spearman" )