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Infer gene set species

Source: R/infer_geneset_species.R
infer_geneset_species.Rd

Infers species from from a gene set using infer_species. If geneset_species is not NULL, this will be returned instead of inferring the species.

Usage

infer_geneset_species(geneset, geneset_species = NULL, verbose = 1, ...)

Arguments

geneset

Genes which are to be tested. Can be gene symbols (or other gene IDs) from any species listed in list_species.

geneset_species

Species that the geneset came from. Can be any species listed in list_species. If geneset_species!="human", the geneset will be converted to 1:1 human orthologs using convert_orthologs.

verbose

Message verbosity.

  • 0 or FALSE : Don't print any messages.

  • 1 or TRUE : Only print messages from MAGMA.Celltyping.

  • 2 or c(TRUE,TRUE) : Print messages from MAGMA.Celltyping and the internal orthogene function.

...

Arguments passed on to orthogene::infer_species

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.

Value

Inferred species name.

Examples

  
geneset <- MAGMA.Celltyping::rbfox_binding
geneset_species <- infer_geneset_species(geneset = geneset)
#> geneset_species=NULL: Inferring species from gene names.
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-9606-homologene.csv.gz
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-9544-homologene.csv.gz
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-10116-homologene.csv.gz
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-10090-homologene.csv.gz
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-7955-homologene.csv.gz
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-7227-homologene.csv.gz
#> Inferred gene set species: mouse