convert_orthologs {orthogene} | R Documentation

## Map genes from one species to another

### Description

Currently supports ortholog mapping between any pair of 700+ species.
Use map_species to return a full list of available organisms.

### Usage

    convert_orthologs(
      gene_df,
      gene_input = "rownames",
      gene_output = "rownames",
      standardise_genes = FALSE,
      input_species,
      output_species = "human",
      method = c("gprofiler", "homologene", "babelgene"),
      drop_nonorths = TRUE,
      non121_strategy = "drop_both_species",
      mthreshold = Inf,
      as_sparse = FALSE,
      sort_rows = FALSE,
      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`. 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"`.
`gene_output` | How to return genes. Options include: `"rownames"` : As row names of `gene_df`. `"colnames"` : As column names of `gene_df`. `"columns"` : As new columns "input_gene", "ortholog_gene" (and "input_gene_standard" if `standardise_genes=TRUE`) in `gene_df`. `"dict"` : As a dictionary (named list) where the names are input_gene and the values are ortholog_gene. `"dict_rev"` : As a reversed dictionary (named list) where the names are ortholog_gene and the values are input_gene.
`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 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.
`drop_nonorths` | Drop genes that don't have an ortholog in the `output_species`.
`non121_strategy` | How to handle genes that don't have 1:1 mappings between `input_species`:`output_species`. Options include: `"drop_both_species" or "dbs" or 1` : Drop genes that have duplicate mappings in either the `input_species` or `output_species` (DEFAULT). `"drop_input_species" or "dis" or 2` : Only drop genes that have duplicate mappings in the `input_species`. `"drop_output_species" or "dos" or 3` : Only drop genes that have duplicate mappings in the `output_species`. `"keep_both_species" or "kbs" or 4` : Keep all genes regardless of whether they have duplicate mappings in either species. `"keep_popular" or "kp" or 5` : Return only the most "popular" interspecies ortholog mappings. 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. `"sum","mean","median","min" or "max"` : When `gene_df` is a matrix and `gene_output="rownames"`, these options will aggregate many-to-one gene mappings (`input_species`-to-`output_species`) after dropping any duplicate genes in the `output_species`.
`mthreshold` | Maximum number of ortholog names per gene to show. Passed to gorth. Only used when `method="gprofiler"` (DEFAULT : `Inf`).
`as_sparse` | Convert `gene_df` to a sparse matrix. Only works if `gene_df` is one of the following classes: `matrix` `Matrix` `data.frame` `data.table` `tibble` If `gene_df` is a sparse matrix to begin with, it will be returned as a sparse matrix (so long as `gene_output=` `"rownames"` or `"colnames"`).
`sort_rows` | Sort `gene_df` rows alphanumerically.
`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

`gene_df` with orthologs converted to the `output_species`.
Instead returned as a dictionary (named list) if `gene_output="dict"` or `"dict_rev"`.

### Examples

    data("exp_mouse")
    gene_df <- convert_orthologs(
        gene_df = exp_mouse,
        input_species = "mouse"
    )

[Package orthogene version 1.0.2 Index]