rdiopt's Introduction

RDIOPT

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.

Installation

You can install the development version of RDIOPT from GitHub with:

# install.packages("devtools")
devtools::install_github("myuhao/RDIOPT")

Example

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"