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 database, e.g., org.Hs.eg.db for human or org.Ms.eg.db for mouse. Input must be of class 'OrgDb'
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 May 10, 2022, 3:42 a.m.