README.md

In keqiang/genemap: Map gene identifiers within or cross species

Package genemap

Map gene identifies within or across species

Usage

map_genes(
  from_species = SPECIES,
  from_id_list,
  from_id_type = c("ensemblgid", "ncbigid", "symbol"),
  to_species = SPECIES,
  to_id_type = c("ensemblgid", "ncbigid", "symbol")
)

# Type genemap::SPECIES to see the full list of supported species
genemap::SPECIES
  Human     Mouse       Rat Zebrafish  Fruitfly
   "hs"      "mm"      "rn"      "dr"      "dm"

Arguments

from_species From which species

from_id_list Gene identifiers to be mapped

from_id_type The type of the identifiers in from_id_list

to_species To which species

to_id_type The type of the identifiers to map to

Examples

Same species mapping

map_genes(
  from_species = "hs",
  from_id_list = c("ENPP4", "GCLC"),
  from_id_type = "symbol",
  to_species = "hs"
)

$ENPP4
$ENPP4$mapped_genes
[1] "ENSG00000001561"

$ENPP4$mapped_gene_symbols
[1] "ENPP4"

$ENPP4$gene_symbol
[1] "ENPP4"


$GCLC
$GCLC$mapped_genes
[1] "ENSG00000001084"

$GCLC$mapped_gene_symbols
[1] "GCLC"

$GCLC$gene_symbol
[1] "GCLC"

Cross-species mapping

map_genes(
  from_species = "hs",
  from_id_list = c("ENPP4", "GCLC"),
  from_id_type = "symbol",
  to_species = "mm",
  to_id_type = "symbol"
)

$ENPP4
$ENPP4$mapped_genes
[1] "Enpp4"


$GCLC
$GCLC$mapped_genes
[1] "Gclc"

keqiang/genemap documentation built on Feb. 5, 2020, 6:53 p.m.