write_subset_ontologies: Write gene ontology tables for data subsets

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

Write gene ontology tables for data subsets

Description

Given a set of ontology results, this attempts to write them to an excel workbook in a consistent and relatively easy-to-read fashion.

Usage

write_subset_ontologies(
  kept_ontology,
  outfile = "excel/subset_go",
  dated = TRUE,
  n = NULL,
  overwritefile = TRUE,
  add_plots = TRUE,
  ...
)

Arguments

kept_ontology	A result from subset_ontology_search()
outfile	Workbook to which to write.
dated	Append the year-month-day-hour to the workbook.
n	How many ontology categories to write for each search
overwritefile	Overwrite an existing workbook?
add_plots	Add the various p-value plots to the end of each sheet?
...	some extra parameters

Value

a set of excel sheet/coordinates

See Also

[openxlsx]

Examples

## Not run: 
 all_contrasts <- all_pairwise(expt, model_batch = TRUE)
 keepers <- list(bob = ('numerator','denominator'))
 kept <- combine_de_tables(all_contrasts, keepers = keepers)
 changed <- extract_significant_genes(kept)
 kept_ontologies <- subset_ontology_search(changed, lengths = gene_lengths,
                                           goids = goids, gff = gff, gff_type='gene')
 go_writer <- write_subset_ontologies(kept_ontologies)

## End(Not run)

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