go_enrich: Gene ontology enrichment analysis of gene clusters.

In charliex210/sctools: Tools for single cell RNAseq analysis

Description

Perform GO analysis using topGO.

Usage

go_enrich(gene_labels, method = "weight01", save_dir = NA, nodeSize = 30,
  showNodes = 15, topNodes = 50, width = 12, height = 10)

Arguments

gene_labels	Data frame of gene names with cluster labels.
method	Test statistics to deal with the GO graph structure - default is weight01, a mixture between the elim and weight algorithms. Alternative algorithms are classic, elim, weight, lea, parentchild. See topGO-package for more detail.
save_dir	Where GO results to be saved. If NA results will be save in the folder called 'GO_results'.
nodeSize	The nodes with less than nodeSize annotated genes are removed from the GO hierarchy
showNodes	How many term to show in the bar plot.
width	Width of the barplot.
height	Height of the barplot.

Value

go_enrich returns a list of:

• the statistic results of each clusters;

• the genes in each term of each cluster.

charliex210/sctools documentation built on Dec. 29, 2021, 11:19 p.m.