Infer CellTypeDataset species — infer_ctd_species • MAGMA.Celltyping

Infers species from from level 1 of a CellTypeDataset (CTD) using either the metadata stored in the CTD (if the object has previously been standardised with standardise_ctd) or using the gene names (via infer_species). If ctd_species is not NULL, this will be returned instead of inferring the species.

Usage

infer_ctd_species(ctd, ctd_species = NULL, verbose = 2, ...)

Arguments

ctd

Cell type data structure containing specificity_quantiles.

ctd_species

Species name relevant to the CellTypeDataset (ctd). See list_species for all available species. If ctd_species=NULL (default), the ctd species will automatically be inferred using infer_species.

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

  
ctd_species <- infer_ctd_species(ctd = ewceData::ctd())
#> see ?ewceData and browseVignettes('ewceData') for documentation
#> loading from cache
#> ctd_species=NULL: Inferring species from gene names.
#> Preparing gene_df.
#> Dense matrix format detected.
#> Extracting genes from rownames.
#> 15,259 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
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-9606-homologene.csv.gz
#> 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
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-9544-homologene.csv.gz
#> 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
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-10116-homologene.csv.gz
#> 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
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-10090-homologene.csv.gz
#> 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
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-7955-homologene.csv.gz
#> 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
#> Using cached file: /github/home/.cache/R/orthogene/all_genes-7227-homologene.csv.gz
#> Returning all 8,438 genes from fly.
#> Top match:
#>   - species: mouse 
#>   - percent_match: 92%
#> Inferred ctd species: mouse