simple_gsva: Provide some defaults and guidance when attempting to use...

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

Provide some defaults and guidance when attempting to use gsva.

Description

gsva seems to hold a tremendous amount of potential. Unfortunately, it is somewhat opaque and its requirements are difficult to pin down. This function will hopefully provide some of the requisite defaults and do some sanity checking to make it more likely that a gsva analysis will succeed.

Usage

simple_gsva(
  expt,
  signatures = "c2BroadSets",
  data_pkg = "GSVAdata",
  signature_category = "c2",
  cores = NULL,
  current_id = "ENSEMBL",
  required_id = "ENTREZID",
  min_catsize = 5,
  orgdb = "org.Hs.eg.db",
  method = "ssgsea",
  kcdf = NULL,
  ranking = FALSE,
  msig_db = NULL,
  wanted_meta = "all",
  mx_diff = TRUE,
  verbose = FALSE,
  id_type = "entrez"
)

Arguments

expt	Expt object to be analyzed.
signatures	Provide an alternate set of signatures (GeneSetCollections)
data_pkg	What package contains the requisite dataset?
signature_category	Specify a subset category to extract from the signatures database.
cores	How many CPUs to use?
current_id	Where did the IDs of the genes come from?
required_id	gsva (I assume) always requires ENTREZ IDs, but just in case this is a parameter.
min_catsize	Minimum category size to consider interesting (passed to gsva()).
orgdb	What is the data source for the rownames()?
method	Which gsva method to use? Changed this from gsva to ssgsea because it was throwing segmentation faults.
kcdf	Options for the gsva methods.
ranking	another gsva option.
msig_db	File contining msigdb annotations.
wanted_meta	Desired metadata elements from the mxig_xml file.
mx_diff	Passed to gsva(), I do not remember what it does.
verbose	Print some information while running?
id_type	Specify the ID type when loading the signature database.

Value

List containing three elements: first a modified expressionset using the result of gsva in place of the original expression data; second the result from gsva, and third a data frame of the annotation data for the gene sets in the expressionset. This seems a bit redundant, perhaps I should revisit it?

See Also

[GSEABase] [load_gmt_signatures()] [create_expt()] [GSVA]

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