Map orthologs

Source: R/map_orthologs.R

Map orthologs from one species to another.

map_orthologs(
  genes,
  standardise_genes = FALSE,
  input_species,
  output_species = "human",
  method = c("gprofiler", "homologene", "babelgene"),
  mthreshold = Inf,
  gene_map = NULL,
  input_col = "input_gene",
  output_col = "ortholog_gene",
  verbose = TRUE,
  ...
)

Arguments

genes

can be a mixture of any format (HGNC, Ensembl, RefSeq, UniProt, etc.) and will be automatically converted to standardised HGNC symbol format.

standardise_genes

If TRUE AND gene_output="columns", a new column "input_gene_standard" will be added to gene_df containing standardised HGNC symbols identified by gorth.

input_species

Name of the input species (e.g., "mouse","fly"). Use map_species to return a full list of available species.

output_species

Name of the output species (e.g. "human","chicken"). Use map_species to return a full list of available 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.

mthreshold

Maximum number of ortholog names per gene to show. Passed to gorth. Only used when method="gprofiler" (DEFAULT : Inf).

gene_map

A data.frame that maps the current gene names to new gene names. This function's behaviour will adapt to different situations as follows:

  • gene_map=<data.frame> :
    When a data.frame containing the gene key:value columns (specified by input_col and output_col, respectively) is provided, this will be used to perform aggregation/expansion.

  • gene_map=NULL and input_species!=output_species :
    A gene_map is automatically generated by map_orthologs to perform inter-species gene aggregation/expansion.

  • gene_map=NULL and input_species==output_species :
    A gene_map is automatically generated by map_genes to perform within-species gene gene symbol standardization and aggregation/expansion.

input_col

Column name within gene_map with gene names matching the row names of X.

output_col

Column name within gene_map with gene names that you wish you map the row names of X onto.

verbose

Print messages.

...

Additional arguments to be passed to gorth or homologene.

NOTE: To return only the most "popular" interspecies ortholog mappings, supply mthreshold=1 here AND set method="gprofiler" above. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs.

For more details, please see here.

Value

Ortholog map data.frame with at least the columns "input_gene" and "ortholog_gene".

Details

map_orthologs() is a core function within convert_orthologs(), but does not have many of the extra checks, such as non121_strategy) and drop_nonorths.

Examples

data("exp_mouse")
gene_map <- map_orthologs(
    genes = rownames(exp_mouse),
    input_species = "mouse")
#> Converting mouse ==> human orthologs using: gprofiler
#> Retrieving all organisms available in gprofiler.
#> Using stored `gprofiler_orgs`.
#> Mapping species name: mouse
#> Common name mapping found for mouse
#> 1 organism identified from search: mmusculus
#> Retrieving all organisms available in gprofiler.
#> Using stored `gprofiler_orgs`.
#> Mapping species name: human
#> Common name mapping found for human
#> 1 organism identified from search: hsapiens