calculate_alternate_genesetlist_complexity: calculate_alternate_genesetlist_complexity

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

Description

This function calculates an alternative complexity score (not described in the paper) of the gene sets in an XGSA data set with respect to a second species. The alternate complexity score is the total number of homology edges between a gene set and another species divides by the total number of genes in a gene set. As such it ranges from 1 to infinity.

Usage

calculate_alternate_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 an alternative complexity score (not described in the paper) of the gene sets in an XGSA data set with respect to a second species. The alternate complexity score is the total number of homology edges between a gene set and another species divides by the total number of genes in a gene set. As such it ranges from 1 to infinity.

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_alternate_genesetlist_complexity(test_mouse_dataset,'drerio')
print(mouse_zebrafish_complexity)

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