do_topgo: An attempt to make topgo invocations a bit more standard.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

An attempt to make topgo invocations a bit more standard.

Description

My function 'simple_topgo()' was excessively long and a morass of copy/pasted fragments. This attempts to simplify that and converge on a single piece of code for all the methodologies provided by topgo.

Usage

do_topgo(
  type,
  go_map = NULL,
  fisher_genes = NULL,
  ks_genes = NULL,
  selector = "topDiffGenes",
  sigforall = TRUE,
  numchar = 300,
  pval_column = "adj.P.Val",
  overwrite = FALSE,
  cutoff = 0.05,
  densities = FALSE,
  pval_plots = TRUE
)

Arguments

type	Type of topgo search to perform: fisher, KS, EL, or weight.
go_map	Mappings of gene and GO IDs.
fisher_genes	List of genes used for fisher analyses.
ks_genes	List of genes used for KS analyses.
selector	Function to use when selecting genes.
sigforall	Provide significance metrics for all ontologies observed, not only the ones deemed statistically significant.
numchar	A limit on characters printed when printing topgo tables (used?)
pval_column	Column from which to extract DE p-values.
overwrite	Overwrite an existing gene ID/GO mapping?
cutoff	Define 'significant'?
densities	Perform gene density plots by ontology?
pval_plots	Print p-values plots as per clusterProfiler?

Value

List of results from the various tests in topGO.

See Also

[topGO]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.