all_ontology_searches: Perform ontology searches given the results of a differential...

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

Perform ontology searches given the results of a differential expression analysis.

Description

This takes a set of differential expression results, extracts a subset of up/down expressed genes; passes them to goseq, clusterProfiler, topGO, GOstats, and gProfiler; collects the outputs; and returns them in a (hopefully) consistent fashion. It attempts to handle the differing required annotation/GOid inputs required for each tool and/or provide supported species in ways which the various tools expect.

Usage

all_ontology_searches(
  de_out,
  gene_lengths = NULL,
  goids = NULL,
  n = NULL,
  z = NULL,
  lfc = NULL,
  p = NULL,
  overwrite = FALSE,
  species = "unsupported",
  orgdb = "org.Dm.eg.db",
  goid_map = "reference/go/id2go.map",
  gff_file = NULL,
  gff_type = "gene",
  do_goseq = TRUE,
  do_cluster = TRUE,
  do_topgo = TRUE,
  do_gostats = TRUE,
  do_gprofiler = TRUE,
  do_trees = FALSE,
  ...
)

Arguments

de_out	List of topTables comprising limma/deseq/edger outputs.
gene_lengths	Data frame of gene lengths for goseq.
goids	Data frame of goids and genes.
n	Number of genes at the top/bottom of the fold-changes to define 'significant.'
z	Number of standard deviations from the mean fold-change used to define 'significant.'
lfc	Log fold-change used to define 'significant'.
p	Maximum pvalue to define 'significant.'
overwrite	Overwrite existing excel results file?
species	Supported organism used by the tools.
orgdb	Provide an organismDbi/Orgdb to hold the various annotation data, in response to the shift of clusterprofiler and friends towards using them.
goid_map	Mapping file used by topGO, if it does not exist then goids_df creates it.
gff_file	gff file containing the annotations used by gff2genetable from clusterprofiler.
gff_type	Column to use from the gff file for the universe of genes.
do_goseq	Perform simple_goseq()?
do_cluster	Perform simple_clusterprofiler()?
do_topgo	Perform simple_topgo()?
do_gostats	Perform simple_gostats()?
do_gprofiler	Perform simple_gprofiler()?
do_trees	make topGO trees from the data?
...	Arguments to pass through in arglist.

Value

a list of up/down ontology results from goseq/clusterprofiler/topgo/gostats, and associated trees.

See Also

[goseq] [clusterProfiler] [topGO] [goStats] [gProfiler] [GO.db]

Examples

## Not run: 
 many_comparisons = limma_pairwise(expt = an_expt)
 tables = many_comparisons$limma
 this_takes_forever = limma_ontology(tables, gene_lengths = lengthdb,
                                     goids = goids_df, z = 1.5, gff_file='length_db.gff')

## End(Not run)

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