README.md
In davetang/romim: R wrapper functions for the OMIM API

README

The romim package can be used to query the OMIM database; it uses the OMIM API. You can install this package using remotes or devtools; the remotes package is a lightweight replacement of the install functions in devtools.

install.packages("remotes")
remotes::install_github('davetang/romim')

library(romim)
help(package = "romim")

Usage

You will need a valid API key, which you can request for on the OMIM API page. Use set_key to use your API key.

library(romim)
Loading required package: XML
Loading required package: magrittr
Loading required package: xml2

# not a real key
set_key('AAAAAAAAAAAAAAAAAAAAAA')

Use get_omim to retrieve an OMIM entry using a MIM number.

omim_result <- get_omim(147920, geneMap = TRUE)

There are several functions for parsing omim_result.

get_gene(omim_result)
# [1] "KMT2D, MLL2, ALR, KABUK1"

get_title(omim_result)
# [1] "KABUKI SYNDROME 1; KABUK1"

get_inheritance(omim_result)
# [1] "Autosomal dominant"

Use the sapply function to query a list of OMIM numbers.

# a list of OMIM IDs
my_list <- list(100070,100100,100300,100600,100800,100820,101000,101200,101400,101600)

my_list_omim <- sapply(my_list, get_omim)
sapply(my_list_omim, get_title)
# [1] "AORTIC ANEURYSM, FAMILIAL ABDOMINAL, 1; AAA1"
# [2] "PRUNE BELLY SYNDROME; PBS"                   
# [3] "ADAMS-OLIVER SYNDROME 1; AOS1"               
# [4] "ACANTHOSIS NIGRICANS"                        
# [5] "ACHONDROPLASIA; ACH"                         
# [6] "ACHOO SYNDROME"                              
# [7] "NEUROFIBROMATOSIS, TYPE II; NF2"             
# [8] "APERT SYNDROME"                              
# [9] "SAETHRE-CHOTZEN SYNDROME; SCS"               
# [10] "PFEIFFER SYNDROME"

Search OMIM disorders associated with a gene of interest.

my_list <- gene_to_omim('TTN')
my_list_omim <- sapply(my_list, get_omim)
sapply(my_list_omim, get_title)
#                                                             604145 
#                               "CARDIOMYOPATHY, DILATED, 1G; CMD1G" 
#                                                             613765 
#                   "CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 9; CMH9" 
#                                                             608807 
# "MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 10; LGMDR10" 
#                                                             603689 
#  "MYOPATHY, MYOFIBRILLAR, 9, WITH EARLY RESPIRATORY FAILURE; MFM9" 
#                                                             611705 
#                                            "SALIH MYOPATHY; SALMY" 
#                                                             600334 
#                          "TIBIAL MUSCULAR DYSTROPHY, TARDIVE; TMD"

Obtain OMIM IDs from a Phenotypic Series ID.

phenotypic_series('PS213600')
# [1] "213600" "615007" "615483" "616413" "618317" "618824"

Search OMIM using free text, which may be useful for searching for OMIM entries using keywords.

my_search <- search_phenotype("Waardenburg Shah syndrome")
omim_list <- sapply(my_search, get_omim, geneMap = TRUE)
sapply(omim_list, get_title)
#                                                                                                              277580 
#                                                                               "WAARDENBURG SYNDROME, TYPE 4A; WS4A" 
#                                                                                                              609136 
# "PERIPHERAL DEMYELINATING NEUROPATHY, CENTRAL DYSMYELINATION, WAARDENBURG SYNDROME, AND HIRSCHSPRUNG DISEASE; PCWH" 
#                                                                                                              611584 
#                                                                               "WAARDENBURG SYNDROME, TYPE 2E; WS2E" 
#                                                                                                              613266 
#                                                                               "WAARDENBURG SYNDROME, TYPE 4C; WS4C" 
#                                                                                                              613712 
#                                                                 "HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 4; HSCR4" 
#                                                                                                              209880 
#                                                                "CENTRAL HYPOVENTILATION SYNDROME, CONGENITAL; CCHS" 
#                                                                                                              613265 
#                                                                               "WAARDENBURG SYNDROME, TYPE 4B; WS4B" 
#                                                                                                              600155 
#                                                                 "HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 2; HSCR2" 
#                                                                                                              600501 
#                                                                                              "ABCD SYNDROME; ABCDS" 
#                                                                                                              142623 
#                                                                 "HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 1; HSCR1" 
#                                                                                                              148820 
#                                                                                 "WAARDENBURG SYNDROME, TYPE 3; WS3" 
#                                                                                                              193500 
#                                                                                 "WAARDENBURG SYNDROME, TYPE 1; WS1" 
#                                                                                                              193510 
#                                                                               "WAARDENBURG SYNDROME, TYPE 2A; WS2A" 
#                                                                                                              613884 
#                                                                                "CHROMOSOME 13q14 DELETION SYNDROME"

How to modify package

The functions are in the R directory and you can modify them as you please. If you modify the documentation in these files, you will need to run document(); see below.

ls -1 R
gene_to_omim.R
get_gene.R
get_inheritance.R
get_omim.R
get_pheno_key.R
get_title.R
phenotypic_series.R
search_phenotype.R
set_key.R

To add more functions, create an .R file inside the R directory; the file should follow the Roxygen process. For example:

#' Set API key
#'
#' This function sets the API key
#' 
#' @param key Your API key
#' @keywords key
#' @export
#' @examples
#' my_key <- set_key('aAS5ASdf35jasdnadsfj') # not a real key

set_key <- function(key){
  my_key <<- paste('apiKey=', key, sep='')
}

After you have added the file (or modified the original files), you'll need to run document().

library(roxygen2)
library(devtools)

# change this to where you cloned the repo
setwd('~/github/romim/')
document()

Then (re-)install the package to see if everything works.

setwd('..')
install("romim")

Troubleshooting

The first version of romim stopped working when the xmlParse function from the XML package was updated. In the latest version of romim (1.0.1), read_xml from the xml2 package is used to retrieve the results. The functions get_omim, gene_to_omim, phenotypic_series, and search_phenotype now includes a show_query parameter that will output the query. You can paste this output to your Internet browser for troubleshooting purposes, to see if any results are retrieved.