simple_gostats: Simplification function for gostats, in the same vein as...

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

Simplification function for gostats, in the same vein as those written for clusterProfiler, goseq, and topGO.

Description

GOstats has a couple interesting peculiarities: Chief among them: the gene IDs must be integers. As a result, I am going to have this function take a gff file in order to get the go ids and gene ids on the same page.

Usage

simple_gostats(
  sig_genes,
  go_db = NULL,
  gff = NULL,
  gff_df = NULL,
  universe_merge = "id",
  second_merge_try = "locus_tag",
  species = "fun",
  pcutoff = 0.1,
  conditional = FALSE,
  categorysize = NULL,
  gff_id = "ID",
  gff_type = "cds",
  excel = NULL,
  ...
)

Arguments

sig_genes	Input list of differentially expressed genes.
go_db	Set of GOids, as before in the format ID/GO.
gff	Annotation information for this genome.
gff_df	I do not remember what this is for.
universe_merge	Column from which to create the universe of genes.
second_merge_try	If the first universe merge fails, try this.
species	Genbank organism to use.
pcutoff	Pvalue cutoff for deciding significant.
conditional	Perform a conditional search?
categorysize	Category size below which to not include groups.
gff_id	key in the gff file containing the unique IDs.
gff_type	Gff column to use for creating the universe.
excel	Print the results to an excel file?
...	More parameters!

Value

List of returns from GSEABase, Category, etc.

See Also

[GSEABase] [Category] [load_gff_annotations()] [GOstats]

Examples

## Not run: 
 knickerbockers <- simple_gostats(sig_genes, gff_file, goids)

## End(Not run)

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