simple_clusterprofiler: Perform the array of analyses in the 2016-04 version of...

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

Perform the array of analyses in the 2016-04 version of clusterProfiler

Description

The new version of clusterProfiler has a bunch of new toys. However, it is more stringent in terms of input in that it now explicitly expects to receive annotation data in terms of a orgdb object. This is mostly advantageous, but will probably cause some changes in the other ontology functions in the near future. This function is an initial pass at making something similar to my previous 'simple_clusterprofiler()' but using these new toys.

Usage

simple_clusterprofiler(
  sig_genes,
  de_table = NULL,
  orgdb = "org.Dm.eg.db",
  orgdb_from = NULL,
  orgdb_to = "ENTREZID",
  go_level = 3,
  pcutoff = 0.05,
  qcutoff = 0.1,
  fc_column = "logFC",
  second_fc_column = "deseq_logfc",
  updown = "up",
  permutations = 1000,
  min_groupsize = 5,
  kegg_prefix = NULL,
  kegg_organism = NULL,
  do_gsea = TRUE,
  categories = 12,
  excel = NULL,
  do_david = FALSE,
  do_kegg = FALSE,
  david_id = "ENTREZ_GENE_ID",
  david_user = "[e-mail]"
)

Arguments

sig_genes	Dataframe of genes deemed 'significant.'
de_table	Dataframe of all genes in the analysis, primarily for gse analyses.
orgdb	Name of the orgDb used for gathering annotation data.
orgdb_from	Name of a key in the orgdb used to cross reference to entrez IDs.
orgdb_to	List of keys to grab from the orgdb for cross referencing ontologies.
go_level	How deep into the ontology tree should this dive for over expressed categories.
pcutoff	P-value cutoff for 'significant' analyses.
qcutoff	Q-value cutoff for 'significant' analyses.
fc_column	When extracting vectors of all genes, what column should be used?
second_fc_column	When extracting vectors of all genes, what column should be tried the second time around?
updown	Include the less than expected ontologies?
permutations	How many permutations for GSEA-ish analyses?
min_groupsize	Minimum size of an ontology before it is included.
kegg_prefix	Many KEGG ids need a prefix before they will cross reference.
kegg_organism	Choose the 3 letter KEGG organism name here.
do_gsea	Perform gsea searches?
categories	How many categories should be plotted in bar/dot plots?
excel	Print the results to an excel file?
do_david	Attempt to use the DAVID database for a search?
do_kegg	Perform kegg search?
david_id	Which column to use for cross-referencing to DAVID?
david_user	Default registered username to use.

Value

a list

See Also

[clusterProfiler] [AnnotationDbi] [KEGGREST]

Examples

## Not run: 
 holyasscrackers <- simple_clusterprofiler(gene_list, all_genes, "org.Dm.eg.db")

## End(Not run)

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