simple_gprofiler_old: Run searches against the web service g:Profiler.

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

Run searches against the web service g:Profiler.

Description

Thank you Ginger for showing me your thesis, gProfiler is pretty cool!

Usage

simple_gprofiler_old(
  sig_genes,
  species = "hsapiens",
  convert = TRUE,
  first_col = "logFC",
  second_col = "limma_logfc",
  do_go = TRUE,
  do_kegg = TRUE,
  do_reactome = TRUE,
  do_mi = TRUE,
  do_tf = TRUE,
  do_corum = TRUE,
  do_hp = TRUE,
  significant = TRUE,
  pseudo_gsea = TRUE,
  id_col = "row.names",
  excel = NULL
)

Arguments

sig_genes	Guess! The set of differentially expressed/interesting genes.
species	Organism supported by gprofiler.
convert	Use gProfileR's conversion utility?
first_col	First place used to define the order of 'significant'.
second_col	If that fails, try a second column.
do_go	Perform GO search?
do_kegg	Perform KEGG search?
do_reactome	Perform reactome search?
do_mi	Do miRNA search?
do_tf	Search for transcription factors?
do_corum	Do corum search?
do_hp	Do the hp search?
significant	Only return the statistically significant hits?
pseudo_gsea	Is the data in a ranked order by significance?
id_col	Which column in the table should be used for gene ID crossreferencing? gProfiler uses Ensembl ids. So if you have a table of entrez or whatever, translate it!
excel	Print the results to an excel file?

Value

List of results for go, kegg, reactome, and a few more.

See Also

[gProfiler]

Examples

## Not run: 
 gprofiler_is_nice_and_easy <- simple_gprofiler(genes, species='mmusculus')

## End(Not run)

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