Infer species from gene names

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.

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.

list

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 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 <- orthogene::infer_species(gene_df = exp_mouse[1:200,])
#> Preparing gene_df.
#> sparseMatrix format detected.
#> Extracting genes from rownames.
#> 200 genes extracted.
#> Testing for gene overlap with: human
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: 9606
#> Gene table with 19,129 rows retrieved.
#> Returning all 19,129 genes from human.
#> Testing for gene overlap with: monkey
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: monkey
#> Common name mapping found for monkey
#> 1 organism identified from search: 9544
#> Gene table with 16,843 rows retrieved.
#> Returning all 16,843 genes from monkey.
#> Testing for gene overlap with: rat
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: rat
#> Common name mapping found for rat
#> 1 organism identified from search: 10116
#> Gene table with 20,616 rows retrieved.
#> Returning all 20,616 genes from rat.
#> Testing for gene overlap with: mouse
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: mouse
#> Common name mapping found for mouse
#> 1 organism identified from search: 10090
#> Gene table with 21,207 rows retrieved.
#> Returning all 21,207 genes from mouse.
#> Testing for gene overlap with: zebrafish
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: zebrafish
#> Common name mapping found for zebrafish
#> 1 organism identified from search: 7955
#> Gene table with 20,897 rows retrieved.
#> Returning all 20,897 genes from zebrafish.
#> Testing for gene overlap with: fly
#> Retrieving all genes using: homologene.
#> Retrieving all organisms available in homologene.
#> Mapping species name: fly
#> Common name mapping found for fly
#> 1 organism identified from search: 7227
#> Gene table with 8,438 rows retrieved.
#> Returning all 8,438 genes from fly.
#> Top match:
#>   - species: mouse 
#>   - percent_match: 96%