sig_ontologies: Take the result from extract_significant_genes() and perform...

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

Take the result from extract_significant_genes() and perform ontology searches.

Description

It can be annoying/confusing to extract individual sets of 'significant' genes from a differential expression analysis. This function should make that process easier.

Usage

sig_ontologies(
  significant_result,
  excel_prefix = "excel/sig_ontologies",
  search_by = "deseq",
  excel_suffix = ".xlsx",
  type = "gprofiler",
  ...
)

Arguments

significant_result	Result from extract_siggenes()
excel_prefix	How to start the output filenames?
search_by	Use the definition of 'significant' from which program?
excel_suffix	How to end the excel filenames?
type	Which specific ontology search to use?
...	Arguments passed to the various simple_ontology() function.

Value

A list of the up/down results of the ontology searches.

See Also

[openxlsx] [simple_goseq()] [simple_clusterprofiler()] [simple_topgo()] [simple_gprofiler()] [simple_topgo()] [simple_gostats()]

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