Prepare the gene set lists collected from various sources

Usage

prepare_gsls(
  gs_sources = NULL,
  custom_gsls = NULL,
  CM_tissues = NULL,
  PNDB_tissues = NULL,
  msigdb_hs_cat_subcat = NULL,
  genes_min = 5,
  genes_max = 500,
  id_type = c("Symbol", "EntrezID"),
  scMuffinList = NULL,
  genes = NULL
)

Arguments

gs_sources: character vector, possible values: "CM_cancer", "CM_normal", "CancerSEA", "PNDB" and "msigdb"
custom_gsls: named list of gene sets
CM_tissues: character vector with strings to filter CellMArker db by tissue name
PNDB_tissues: character vector with strings to filter Panglao db by tissue name
msigdb_hs_cat_subcat: data.frame with species, category and subcategory: e.g. "Homo sapiens", "NA", "CP:KEGG"
genes_min: minimum number of genes required in a gene set
genes_max: maximum number of genes required in a gene set
id_type: type of id: Symbol or EntrezID
scMuffinList: scMuffinList object
genes: all genes to be considered

Value

A lists of gene set lists