inst/extdata/Unused_R_Functions/get_ACMG.R

In jamesdiao/clinvaR: collection, analysis, and visualization tools for ClinVar data

#' Scrape ACMG Table from ClinVar
#'
#' This function scrapes the table from 'https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg' and cleans it up. 
#' Columns are: Disease, MedGen, Gene, Variations_Link.
#' 
#' @usage scrape_ACMG()
#' @keywords ACMG
#' #@export

scrape_ACMG <- function() {
  ACMG.page <- scrapeR::scrape(url ="https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/")[[1]]
  ACMG.table <- readHTMLTable(ACMG.page, stringsAsFactors = F, header = T)[[1]]
  colnames(ACMG.table) <- c("Disease", "MedGen","Gene","Variations_Link")
  ### Formatting correction: separating merged gene blocks
  badrow <- which(apply(ACMG.table, 1, function(row) !any(grepl("ClinVar", row))))
  ACMG.table[badrow,"Gene"] <- ACMG.table[badrow-1,"Gene"]
  ### Formatting corrections: sliding
  mismatch <- 0
  while(any(ACMG.table[,"Gene"] == "ClinVar")) {
    mismatch <- which(ACMG.table[,"MedGen"]!="MedGen")
    ACMG.table[mismatch,2:3] <- ACMG.table[mismatch,1:2]
    for (row in mismatch) { ACMG.table[row,"Disease"] <- ACMG.table[row-1, "Disease"] }
  }
  ACMG.table %>% select(Disease, Gene) %>% 
    separate(col = Disease, into = c("Disease_Name","Disease_MIM"), sep = " \\(MIM ") %>%
    separate(col = Gene, into = c("Gene_Name","Gene_MIM"), sep = " \\(MIM ") %>% 
    mutate(Disease_MIM = strsplit(Disease_MIM, "\\)") %>% sapply("[",1)) %>%
    mutate(Gene_MIM = strsplit(Gene_MIM, "\\)") %>% sapply("[",1))
  return(ACMG.table)
}


#' Import ACMG Table from Data
#'
#' This function imports Table 1 of the ACMG SF v2.0 paper
#' (http://www.nature.com/gim/journal/v19/n2/abs/gim2016190a.html)
#' and separates listed entries by the pipe delimiter. 
#' 
#' Columns are: Phenotype, MIM_disorder, PMID_Gene_Reviews_entry, Typical_age_of_onset, 
#' Gene, MIM_gene, Inheritance, Variants_to_report
#' 
#' The file is stored in inst/extdata. 
#' 
#' @usage import_ACMG()
#' @keywords ACMG
#' @export
#' 

import_ACMG <- function() {
  ACMG.table <- system.file("extdata", "Supplementary_Files/ACMG_SF_v2.0.txt", package = "clinvaR") %>% 
    read.table(stringsAsFactors = F, sep = "\t", header = T) %>%
    mutate(Gene = strsplit(Gene, "|", fixed = T)) %>% 
    mutate(MIM_gene = strsplit(MIM_gene, "|", fixed = T)) %>% 
    mutate(Inheritance = strsplit(Inheritance, "|", fixed = T)) %>% 
    mutate(Variants_to_report = strsplit(Variants_to_report, "|", fixed = T)) %>% 
    unnest()
  return(ACMG.table)
}

#' Prints list of 59 ACMG genes
#'
#' This function calls import_ACMG() and extracts the `Gene` column. 
#' 
#' @usage ACMG_genes()
#' @keywords ACMG
#' @export
#' 

ACMG_genes <- function() {
  tbl <- import_ACMG()
  return(tbl$Gene)
}