Calculate gene set score at cluster level

Usage

calculate_gs_scores_in_clusters(
  scMuffinList = NULL,
  partition_id = NULL,
  ncells_min = 5,
  alt = "g",
  test = "t",
  fract_min = 0.5
)

Arguments

scMuffinList: scMuffinList object
partition_id: identifier of the partition to be used
ncells_min: minimum number of cells required for the calculation of the average signature in the cluster
alt: alterative passed to [wilcox.test()] or [t.test()]
test: type of test: t to use [t.test()]; wrs to use [wilcox.test()]
fract_min: only clusters with this fraction of cells with not null gene set score will be considered

Value

scMuffinList with cluster level scores in `sMuffinList$cluster_data[[partition_id]]`. The element [summary] contains a clusters-by-gene sets table, while the element [full] the full result