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 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")

[Package orthogene version 1.0.2 Index]