infer_ctd_species: Infer CellTypeDataset species

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Infer CellTypeDataset species

Description

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. 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 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())

NathanSkene/MAGMA_Celltyping documentation built on Aug. 21, 2023, 8:55 a.m.