estimateOntologyFromIds: Calculate ontologies based on DEs

In kharchenkolab/cacoa: Case-Control Analysis Tools for Single-Cell RNA-Seq

Calculate ontologies based on DEs

Description

Calculate ontologies based on DEs

Usage

estimateOntologyFromIds(
  de.gene.scores,
  go.environment,
  type = "GO",
  org.db = NULL,
  n.top.genes = 500,
  keep.gene.sets = FALSE,
  verbose = TRUE,
  n.cores = 1,
  ...
)

Arguments

de.gene.scores	input DE gene scores
go.environment	GO environment set (Homo sapiens, Mus musculus, etc.)
type	character string Ontology type, either GO (gene ontology) or DO (disease ontology) (default="GO") Please see DOSE package for more information.
org.db	organism db, e.g. org.Hs.eg.db::org.Hs.eg.db
n.top.genes	numeric Number of most different genes to take as input. If less are left after filtering for p.adj.cutoff, additional genes are included. To disable, set n.top.genes=0 (default=1e2)
keep.gene.sets	boolean Keep gene sets (default=FALSE)
verbose	boolean Print progress (default=TRUE)
n.cores	integer Number of cores (default=1)
...	Additional parameters for DO/GO/GSEA functions. In case of GSEA, pass nPerm to call fgseaSimple instead of fgseaMultilevel

Value

A list containing a list of ontologies per type of ontology, and a data frame with merged results

kharchenkolab/cacoa documentation built on Nov. 8, 2024, 6:06 a.m.