calculate_genesetlist_complexity: calculate_genesetlist_complexity

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

Description

This helper function calculates the complexity score of the gene sets in an XGSA data set with respect to a second species. The complexity score is defined in the publication, as the fraction of gene set that has complex homology to another species.

Usage

calculate_genesetlist_complexity(dataset, species2)

Arguments

dataset	An XGSA data set created by 'new_XGSA_dataset'
species2	Species name in the form 'hsapiens', naming the species to compare the dataset against for gene set complexity.

Details

This function calculates the complexity score of the gene sets in an XGSA data set with respect to a second species. The complexity score is defined in the publication, as the fraction of gene set that has complex homology to another species.

Value

This function returns a list of complexity scores, one score for each gene set

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')
mouse_zebrafish_complexity <- calculate_genesetlist_complexity(test_mouse_dataset,'drerio')
print(mouse_zebrafish_complexity)

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