infer_species {orthogene} | R Documentation

## Infer species from gene names

### Description

Infers which species the genes within `gene_df` is from. Iteratively test the percentage of `gene_df` genes that match with the genes from each `test_species`.

### Usage

    infer_species(
      gene_df,
      gene_input = "rownames",
      test_species = c("human", "monkey", "rat", "mouse", "zebrafish", "fly"),
      method = c("homologene", "gprofiler", "babelgene"),
      make_plot = TRUE,
      show_plot = TRUE,
      verbose = TRUE
    )

### Arguments

`gene_df` | Data object containing the genes (see `gene_input` for options on how the genes can be stored within the object). Can be one of the following formats: `matrix` : A sparse or dense matrix. `data.frame` : A `data.frame`, `data.table`. or `tibble`. codelist : A `list` or character `vector`. Genes, transcripts, proteins, SNPs, or genomic ranges can be provided in any format (HGNC, Ensembl, RefSeq, UniProt, etc.) and will be automatically converted to gene symbols unless specified otherwise with the `...` arguments. Note: If you set `method="homologene"`, you must either supply genes in gene symbol format (e.g. "Sox2") OR set `standardise_genes=TRUE`.
`gene_input` | Which aspect of `gene_df` to get gene names from: `"rownames"` : From row names of data.frame/matrix. `"colnames"` : From column names of data.frame/matrix. `<column name>` : From a column in `gene_df`, e.g. `"gene_names"`.
`test_species` | Which species to test for matches with. If set to `NULL`, will default to a list of humans and 5 common model organisms. If `test_species` is set to one of the following options, it will automatically pull all species from that respective package and test against each of them: "homologene"20+ species (default) "gprofiler"700+ species "babelgene"19 species
`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.
`make_plot` | Make a plot of the results.
`show_plot` | Print the plot of the results.
`verbose` | Print messages.

### Value

An ordered dataframe of `test_species` from best to worst matches.

### Examples

    data("exp_mouse")
    matches <- infer_species(gene_df = exp_mouse[1:200,])

[Package orthogene version 1.0.2 Index]