Gene Set Enrichment Analysis

Usage

csea(
  rl = NULL,
  gsl = NULL,
  k = 99,
  min.size = 100,
  ord.mode = -1,
  min.k = 10,
  mc_cores_path = 1,
  mc_cores_perm = 1,
  fract_min = 0.2
)

Arguments

rl: numeric matrix of genes-by-ranking criteria; each column contains numeric values; rownames are mandatory
gsl: named list of gene sets
k: number of permutations
min.size: minimum number of cells with a not null value
ord.mode: ordering mode: -1 -> descending; 1 ascending; must be of length equal to `ncol(rl)`
min.k: minimum number of valid permutations to support empirical nulls
mc_cores_path: number of cores to use for parallel calculation of gene set lists; the total number of cpu used will be mc_cores_path * mc_cores_perm
mc_cores_perm: number of cores to use for parallel calculation of ranked list permutations; the total number of cpu used will be mc_cores_path * mc_cores_perm
fract_min: only cluster of size less or equal to this fraction of cell with not null feature values will be analysed

Value

list with two data.frames, gs_table and leading_edge.