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 = "",
  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).

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 0.99.9 Index]