simple_gprofiler2: 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

This is the beginning of a reimplementation to use gprofiler2. However, AFAICT gprofiler2 does not yet actually work for anything other than their GO data.

Usage

simple_gprofiler2(
  sig_genes,
  species = "hsapiens",
  convert = TRUE,
  first_col = "deseq_logfc",
  second_col = "logfc",
  do_go = TRUE,
  do_kegg = TRUE,
  do_reactome = TRUE,
  do_mi = TRUE,
  do_tf = TRUE,
  do_corum = TRUE,
  do_hp = TRUE,
  do_hpa = TRUE,
  do_wp = TRUE,
  significant = TRUE,
  exclude_iea = FALSE,
  do_under = FALSE,
  evcodes = TRUE,
  threshold = 0.05,
  adjp = "g_SCS",
  domain_scope = "annotated",
  bg = NULL,
  pseudo_gsea = TRUE,
  id_col = "row.names",
  plot_type = "dotplot",
  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?
do_hpa	Do the hpa search?
do_wp	Do the wp search?
significant	Only return the statistically significant hits?
exclude_iea	Passed directly to gprofiler2.
do_under	Perform under-representation search?
evcodes	Get the set of evcodes in the data? This makes it take longer.
threshold	p-value 'significance' threshold.
adjp	Method to adjust p-values.
domain_scope	Passed to gprofiler2.
bg	Background genes.
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!
plot_type	Use this plot type for images.
excel	Print the results to an excel file?

Value

a 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.