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.
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).
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
#> 6 12 NP_000017.1 XP_003317301.1
#> 7 13 NP_000018.2 XP_517545.2
#> 8 14 NP_000020.1 NP_001009032.1
#> 9 16 NP_000022.3 XP_001152445.2
#> 10 17 NP_000023.2 XP_528998.2
#> # ℹ 17,727 more rows
# # 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