Skip to contents

Assess enrichment with ORA or CSEA

assess_cluster_enrichment.Rd

Assess cluster enrichment using ORA for categorical features and CSEA for numeric features.

Usage

assess_cluster_enrichment(
  scMuffinList = NULL,
  feature_name = NULL,
  partition_id = NULL,
  min.cells.feature = 100,
  min.cells.cluster = 10,
  fract_min = 0.2,
  mc.cores = 1,
  csea.k = 99,
  min.k = 10
)

Arguments

scMuffinList

scMuffinList list

feature_name

the names of the feature that should be considered. It must be one of names(scMuffinList)

partition_id

identifier of the partition to be considered

min.cells.feature

minimum number of cells in which a feature must have value

min.cells.cluster

minimum number of cells of a cluster

fract_min

only cluster of size less or equal to this fraction of cell with not null feature values will be analysed

mc.cores

number of cores

csea.k

number of CSEA permutations

min.k

minimum number of valid permutations to support empirical nulls

Value

scMuffinList with CSEA or ORA elements under scMuffinList$cluster_data for the considered partition

Details

The output of CSEA is a table with statistics for every tested gene set. The output of ORA is composed of a series of tables with enrichment results, one for every possible categorical value. See [extract_cluster_enrichment_table] to extract summary table from CSEA and ORA results.