data-raw/allele_frequencies.R

In Genentech/MiDAS: R package for immunogenomics data handling and association analysis

#!/usr/bin/env R
# Download HLA frequencies from http://www.allelefrequencies.net/
devtools::load_all()
library("rvest")
library("xml2")

midas_var_hla_locus_vector <-
  c("A", "B", "C", "DQA1", "DQB1", "DPA1", "DPB1", "DRB1", "DRB3", "DRB4", "DRB5")
base_url <- "http://www.allelefrequencies.net/hla6006a.asp?"
qloci <- "hla_locus="
tab_list <- list()
for (loci in midas_var_hla_locus_vector) {
  i <- 1
  query <- paste0(base_url, "page=", as.character(i), "&", qloci, loci)
  res <- xml2::read_html(query)
  node <- rvest::html_node(res, xpath = "//*[@id='divGenDetail']/table")
  if (is.na(node)) next()
  tab <-  rvest::html_table(node)
  colnames(tab) <-
    gsub("[[:blank:]]+", " ", gsub("[^a-zA-Z%() ]", "", colnames(tab)))
  while (! is.na(node) && nrow(tab) > 0) {
    tab_list[[length(tab_list) + 1]] <- tab
    i <- i + 1
    query <- paste0(base_url, "page=", as.character(i), "&", qloci, loci)
    res <- xml2::read_html(query)
    node <- rvest::html_node(res, xpath = "//*[@id='divGenDetail']/table")
    tab <- rvest::html_table(node)
    colnames(tab) <-
      gsub("[[:blank:]]+", " ", gsub("[^a-zA-Z%() ]", "", colnames(tab)))
  }
}

tab_total <- do.call(rbind, tab_list)
# Some cols contains NA other links to external website
i_na <- vapply(tab_total, function(x) length(unique(x)) == 1, logical(1))
allelefrequency_df <- tab_total[, ! i_na]
# 'Line' column specifies record number in search results
allelefrequency_df <-
  allelefrequency_df[, colnames(allelefrequency_df) != "Line"]
colnames(allelefrequency_df) <-
  c("var", "population", "proc.ind.with.allele", "frequency", "sample.size")

# Allele Frequencies marked with (*) were calculated from all alleles in the corresponding G group.
# These symbols can be found in "proc.ind.with.allele", "frequency" columns
star_cols <- c("proc.ind.with.allele", "frequency")
new_star_cols <-
  c(
    "proc.ind.with.allele",
    "proc.ind.with.allele.ggroup",
    "frequency",
    "frequency.ggroup"
  )
ggroup_cols <- c("proc.ind.with.allele.ggroup", "frequency.ggroup")
data.table::setDT(allelefrequency_df)
allelefrequency_df[,
                   (new_star_cols) := unlist(
                     lapply(
                       X = .SD,
                       FUN = function(x) {
                         data.table::tstrsplit(x,
                                               split = " ",
                                               fixed = TRUE,
                                               type.convert = TRUE
                         )
                       }
                     ),
                     recursive = FALSE
                   ),
                   .SDcols =  star_cols
                   ][,
                     (ggroup_cols) := lapply(
                       X = .SD,
                       FUN = function(x) {
                         ! is.na(x)
                       }
                     ),
                     .SDcols = ggroup_cols
                     ][,
                       sample.size := as.numeric(gsub(",", "", sample.size))
                       ]
data.table::setDF(allelefrequency_df)

# order columns
allele_frequencies <-
  allelefrequency_df[, c(
    "var",
    "population",
    "frequency"
    # "frequency.ggroup",
    # "sample.size",
    # "proc.ind.with.allele",
    # "proc.ind.with.allele.ggroup"
  )]

usethis::use_data(allele_frequencies, overwrite = TRUE)