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Extract the top results of CSEA and ORA for each cluster

extract_cluster_enrichment_tags.Rd

Extract the best results of CSEA and ORA for each cluster.

Usage

extract_cluster_enrichment_tags(
  scMuffinList = NULL,
  partition_id = NULL,
  CSEA_selection_criterion = "FDRq",
  CSEA_selection_threshold = 0.25,
  only_pos_nes = TRUE,
  ORA_selection_criterion = "p_adj",
  ORA_selection_threshold = 0.1,
  n_max_per_cluster = 3
)

Arguments

scMuffinList

scMuffinList object.

partition_id

one among the partitions.

CSEA_selection_criterion

selection criteria for results of CSEA. See extract_cluster_enrichment_table for possible values.

CSEA_selection_threshold

threshold for selection of tags from CSEA.

only_pos_nes

whether only positive nes should be considered in CSEA.

ORA_selection_criterion

selection criteria for results of ORA. See extract_cluster_enrichment_table for possible values.

ORA_selection_threshold

threshold for selection of tags from ORA.

n_max_per_cluster

maximum number of tags per cluster.

Value

Add or overwrite the "cluster_tags" list to `scMuffinList$cluster_data[[partition_id]]`