RDIOPT is a simple wrapper around the DIOPT Ortholog Finder. The intention for this package is to allow querying orthologs from R directly, without copy and paste.
RDIOPT relies on the DIOPT API to query and search results.
You can install the development version of RDIOPT from GitHub with:
# install.packages("devtools")
devtools::install_github("myuhao/RDIOPT")
Call find_orthologs()
with some of your gene of interests. The
function should give you a nice tibble
with all the relevant
information.
# Entrez ID always work
gene_of_interests = c(1232, 7316)
# if you have AnnotationDbi installed, the function converts it for you
if (require(org.Hs.eg.db)) {
gene_of_interests = c("CCR3", "UBC")
}
orthologs = RDIOPT::find_orthologs(gene_of_interests, from = 9606, to = 7227, filter = "none")
colnames(orthologs)
#> [1] "date" "search_gene_entrez"
#> [3] "filter" "from_entrez_geneid"
#> [5] "symbol" "description"
#> [7] "chromosome" "gene_type"
#> [9] "ensembl_geneid" "diopt_version"
#> [11] "from_id" "to_id"
#> [13] "to_symbol" "confidence"
#> [15] "score" "best_score"
#> [17] "max_score" "best_score_rev"
#> [19] "best_score_count" "mist_ppi"
#> [21] "mist_genetic" "to_entrez_geneid"
#> [23] "species_id" "species_specific_geneid"
#> [25] "species_specific_geneid_type" "count"
#> [27] "methods"
The result table has many relevant information, but it can be summarized in to three categories:
- Function parameters.
- Source gene information.
- Target gene information.