create_background {orthogene} | R Documentation |
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 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
(slower but more species and genes) or
"homologene" (faster but fewer species and genes).
|
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")
[Package
orthogene version 1.0.0
Index]