simple_topgo: Perform a simplified topgo analysis.

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

Perform a simplified topgo analysis.

Description

This will attempt to make it easier to run topgo on a set of genes. The way I organized these data structures is completely stupid. I want to convert the data from topgo to clusterprofiler for ease of plotting, but because of the terrible way I organized everything that is likely to be difficult.

Usage

simple_topgo(
  sig_genes,
  goid_map = "id2go.map",
  go_db = NULL,
  pvals = NULL,
  limitby = "fisher",
  limit = 0.1,
  signodes = 100,
  sigforall = TRUE,
  numchar = 300,
  selector = "topDiffGenes",
  pval_column = "deseq_adjp",
  overwrite = FALSE,
  densities = FALSE,
  pval_plots = TRUE,
  excel = NULL,
  ...
)

Arguments

sig_genes	Data frame of differentially expressed genes, containing IDs any other columns.
goid_map	File containing mappings of genes to goids in the format expected by topgo.
go_db	Data frame of the goids which may be used to make the goid_map.
pvals	Set of pvalues in the DE data which may be used to improve the topgo results.
limitby	Test to index the results by.
limit	Ontology pvalue to use as the lower limit.
signodes	I don't remember right now.
sigforall	Provide the significance for all nodes?
numchar	Character limit for the table of results.
selector	Function name for choosing genes to include.
pval_column	Column from which to acquire scores.
overwrite	Yeah I do not remember this one either.
densities	Densities, yeah, the densities...
pval_plots	Include pvalue plots of the results a la clusterprofiler?
excel	Print the results to an excel file?
...	Other options which I do not remember right now!

Value

Big list including the various outputs from topgo

See Also

[topGO]

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