new_XGSA_dataset: new_XGSA_dataset

In VCCRI/XGSA: XGSA: A statistical method for cross-species gene set analysis

Description

This function creates an XGSA data set object that is required for performing tests.

Usage

new_XGSA_dataset(species, data, type = "genesetlist", name,
  universe = "empty")

Arguments

species	Species name, in the form 'hsapiens'
data	A named list of gene sets where each element contains a character vector of Ensembl gene IDs. This can be a named list of only a single element containing gene IDs.
type	The type of data provided, currently only 'genesetlist' is supported.
name	A name for the data set / collection of gene sets
universe	The gene universe for the gene sets in data. They must all have the same gene universe. If no gene universe is provided (default) all Ensembl gene IDs for the indicated species will be used as the gene universe.

Details

This function creates an XGSA data set object that is required for performing tests.

Value

This function returns a list with 5 elements describing the data set, the species, gene sets, data type, name of data set and the applicable gene universe.

Examples

test_mouse_genes <- c("ENSMUSG00000033837", "ENSMUSG00000031965", "ENSMUSG00000053110", "ENSMUSG00000030557", "ENSMUSG00000051159", "ENSMUSG00000040289", "ENSMUSG00000035458", "ENSMUSG00000028780", "ENSMUSG00000062327", "ENSMUSG00000037868")
test_mouse_dataset <- new_XGSA_dataset(species = 'mmusculus', data = list(test_genes = test_mouse_genes), name = 'Test Mouse Genes')
print(summary(test_mouse_dataset))

VCCRI/XGSA documentation built on March 5, 2021, 10:22 p.m.