map_genes {orthogene} | R Documentation

## Map genes

### Description

Input a list of genes, transcripts, proteins, SNPs, or genomic ranges in any format (HGNC, Ensembl, RefSeq, UniProt, etc.) and return a table with standardised gene symbols (the "names" column).

### Usage

    map_genes(
      genes,
      species = "hsapiens",
      target = "ENSG",
      mthreshold = Inf,
      drop_na = FALSE,
      numeric_ns = "",
      run_map_species = TRUE,
      verbose = TRUE
    )

### Arguments

`genes` | Gene list.
`species` | Species to map against.
`target` | target namespace.
`mthreshold` | maximum number of results per initial alias to show. Shows all by default.
`drop_na` | Drop all genes without mappings. Sets `gprofiler2::gconvert(filter_na=)` as well an additional round of more comprehensive `NA` filtering by orthogene.
`numeric_ns` | namespace to use for fully numeric IDs (list of available namespaces).
`run_map_species` | Run map_species on `species` first.
`verbose` | Print messages.

### Details

Uses gconvert. The exact contents of the output table will depend on `target` parameter. See `?gprofiler2::gconvert` for more details.

### Value

Table with standardised genes.

### Examples

    genes <- c(
        "Klf4", "Sox2", "TSPAN12", "NM_173007", "Q8BKT6",
        "ENSMUSG00000012396", "ENSMUSG00000074637"
    )
    mapped_genes <- map_genes(
        genes = genes,
        species = "mouse"
    )

[Package orthogene version 1.0.2 Index]