Extract cluster enrichment table — extract_cluster_enrichment

Extract cluster enrichment table with the desired quantity from the results generated by means of [assess_cluster_enrichment()]

Usage

extract_cluster_enrichment_table(
  scMuffinList,
  partition_id = NULL,
  type = NULL,
  quantity = NULL,
  feature_id = NULL
)

scMuffinList: scMuffinList object
partition_id: id of the partition to be used
type: "CSEA" or "ORA"
quantity: possible values are as follows. CSEA: es, enrichment score; p_val empirical p-value; adj_p_val, FDR (BH); nes normalized enrichment score; FDRq empirical FDR. ORA: wbd (white balls drawn), number of cells with the value of interest in the cluster; exp expected number of cells with the value of interest in the cluster; er, enrichment ratio; p, hypergeometric test p-value; p_adj, BH FDR
feature_id: name of the features that will be considered. Must be any of `colnames(scMuffinList$cluster_data$[[parition_id]]$CSEA)` or `names(scMuffinList$cluster_data$[[parition_id]]$ORA)`

A cluster enrichment table with the desired quantity