find_rank_bias {clustifyr} | R Documentation |
Find rank bias
find_rank_bias( mat, metadata, type_col, ref_mat, query_genes = NULL, filter_out = TRUE, threshold = 0.33, expr_cut = 3000, consensus_cut = 1 )
mat |
original query expression matrix |
metadata |
metadata after calling types |
type_col |
column name in metadata that contains ids |
ref_mat |
reference expression matrix |
query_genes |
original vector of genes used to clustify |
filter_out |
whether to only report filtered results |
threshold |
diff threshold |
expr_cut |
consider all lower expressing genes as off |
consensus_cut |
filter out if lower han number of types show large diff |
matrix of rank diff values
res <- clustify( input = pbmc_matrix_small, metadata = pbmc_meta, ref_mat = cbmc_ref, query_genes = pbmc_vargenes, cluster_col = "classified" ) call1 <- cor_to_call( res, metadata = pbmc_meta, cluster_col = "classified", collapse_to_cluster = FALSE, threshold = 0.8 ) pbmc_meta2 <- call_to_metadata( call1, pbmc_meta, "classified" ) find_rank_bias( pbmc_matrix_small, pbmc_meta2, "type", cbmc_ref, query_genes = pbmc_vargenes )