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Orthology table for a pair of organisms

Source: R/homologene.R
homologene_download.Rd

Orthologous pairs of genes for a pair of organisms from NCBI HomoloGene, using one identifier type.

Usage

homologene_download(
  target = 10090L,
  source = 9606L,
  id_type = "genesymbol",
  hgroup_size = FALSE
)

Arguments

target

Character or integer: name or ID of the target organism.

source

Character or integer: name or ID of the source organism.

id_type

Symbol or character: identifier type, possible values are "genesymbol", "entrez", "refseqp" or "gi".

hgroup_size

Logical: include a column with the size of the homology groups. This column distinguishes one-to-one and one-to-many or many-to-many mappings.

Value

A data frame with orthologous identifiers between the two organisms.

Details

The operation of this function is symmetric, *source* and *target* are interchangeable but determine the column layout of the output. The column "hgroup" is a numberic identifier of the homology groups. Most of the groups consist of one pair of orthologous genes (one-to-one mapping), and a few of them multiple ones (one-to-many or many-to-many mappings).

See also

Examples

chimp_human <- homologene_download(chimpanzee, human, refseqp)
chimp_human
# # A tibble: 17,737 × 3
#    hgroup refseqp_source refseqp_target
#     <int> <chr>          <chr>
#  1      3 NP_000007.1    NP_001104286.1
#  2      5 NP_000009.1    XP_003315394.1
#  3      6 NP_000010.1    XP_508738.2
#  4      7 NP_001096.1    XP_001145316.1
#  5      9 NP_000014.1    XP_523792.2
# # . with 17,732 more rows