create_background: Create gene background

In neurogenomics/orthogene: Interspecies gene mapping

Create gene background

Description

Create a gene background as the union/intersect of all orthologs between input species (species1 and species2), and the output_species. This can be useful when generating random lists of background genes to test against in analyses with data from multiple species (e.g. enrichment of mouse cell-type markers gene sets in human GWAS-derived gene sets).

Usage

create_background(
  species1,
  species2,
  output_species = "human",
  as_output_species = TRUE,
  use_intersect = TRUE,
  bg = NULL,
  gene_map = NULL,
  method = "homologene",
  non121_strategy = "drop_both_species",
  verbose = TRUE
)

Arguments

species1	First species.
species2	Second species.
output_species	Species to convert all genes from species1 and species2 to first. Default="human", but can be to either any species supported by orthogene, including species1 or species2.
as_output_species	Return background gene list as output_species orthologs, instead of the gene names of the original input species.
use_intersect	When species1 and species2 are both different from output_species, this argument will determine whether to use the intersect (TRUE) or union (FALSE) of all genes from species1 and species2.
bg	User supplied background list that will be returned to the user after removing duplicate genes.
gene_map	User-supplied gene_map data table from map_orthologs or map_genes.
method	R package to use for gene mapping: "gprofiler" : Slower but more species and genes. "homologene" : Faster but fewer species and genes. "babelgene" : Faster but fewer species and genes. Also gives consensus scores for each gene mapping based on a several different data sources.
non121_strategy	How to handle genes that don't have 1:1 mappings between input_species:output_species. Options include: "drop_both_species" or "dbs" or 1 : Drop genes that have duplicate mappings in either the input_species or output_species (DEFAULT). "drop_input_species" or "dis" or 2 : Only drop genes that have duplicate mappings in the input_species. "drop_output_species" or "dos" or 3 : Only drop genes that have duplicate mappings in the output_species. "keep_both_species" or "kbs" or 4 : Keep all genes regardless of whether they have duplicate mappings in either species. "keep_popular" or "kp" or 5 : Return only the most "popular" interspecies ortholog mappings. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs. "sum","mean","median","min" or "max" : When gene_df is a matrix and gene_output="rownames", these options will aggregate many-to-one gene mappings (input_species-to-output_species) after dropping any duplicate genes in the output_species.
verbose	Print messages.

Value

Background gene list.

Examples

bg <- orthogene::create_background(species1 = "mouse", 
                                   species2 = "rat",
                                   output_species = "human")

neurogenomics/orthogene documentation built on Jan. 30, 2024, 4:44 a.m.