go_enrich: Gene ontology enrichment analysis of gene clusters.

Description Usage Arguments Value

View source: R/GenePattern.R

Description

Perform GO analysis using topGO.

Usage

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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:


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