GOannotation: Compute the weighted GO enrichment of cluster-specific...

In elimereu/matchSCore2: What the Package Does TODOELI

Description

This function computes the weighted GO enrichment across computational gene markers by using their p-values.

Usage

GOannotation(
  markers,
  go.db,
  species = "mouse",
  ontology.type = "BP",
  reformat.gene.names = FALSE,
  go.score.class = "weight01Score",
  p.val.threshold = 0.05,
  dag.file.prefix = FALSE,
  ngenes = 20,
  verbose = TRUE
)

Arguments

markers	A data.frame of cluster specific gene markers like in the Seurat output of the function FindAllMarkers. The used columns are c("p_val","cluster","gene")
go.db	Human (org.Hs.eg.db) or mouse (org.Mm.eg.db) GO database. Corresponding R packages have to be installed.
species	character indicating the species. Only 'human' or 'mouse'.
ontology.type	Ontology family to be examined ("BP"= 'Biological Process', "MF"='Molecular Function', "CC"='Cellular Component')
reformat.gene.names	TODO
go.score.class	TODO
p.val.threshold	TODO
dag.file.prefix	TODO
ngenes	TODO
verbose	Logical, controls the displaying of additional messages while running the function. Defaults to TRUE.

Value

A list with two elements:

• GOenrich contains data.frames with GO enrichments for each cluster.

• genes_byGO provides the set of genes from each resulting GO pathway that are in overlap between your data and the pathway.

Examples

# TODO

elimereu/matchSCore2 documentation built on April 9, 2020, 5:41 p.m.