R/parse_omim.R

In bwzee/favor-gene-build: FAVOR Gene annotation builder

#Parse OMIM phenotypes

library(tidyverse)
library(data.table)


#OMIM Parser
#' Title
#'
#' @param omimfile
#'
#' @return
#' @export
#'
#' @examples
parse_omim<-function(omimfile="../omim/genemap2.txt"){

fread(omimfile,skip = 3,sep="\t",fill=T) %>% janitor::clean_names() %>% as_tibble() ->omim



omim %>% rowwise() %>% mutate(pheno=get_pheno(phenotypes)$phenotype,
                              pheno_mimid=get_pheno(phenotypes)$mimid,
                              pheno_key=get_pheno(phenotypes)$phenokey,
                              inheritance=get_pheno(phenotypes)$inheritance,
                              pheno_disease=get_pheno(phenotypes)$disease
                              )->omim
omim %>% separate(gene_symbols,c("gene_symbol","gene_symbol2"),sep=",",extra="drop",fill="right") ->omim
saveRDS(omim,"omim.rds")

return(omim)
}




# Gwas cat . < 1e-8 -> high confidence----
#' Title
#'
#' @param infile
#'
#' @return
#' @export
#'
#' @examples
parse_gwascat<-function(infile="../GWAS_catalog/gwas_catalog_v1.0.2-associations_e100_r2021-03-25.tsv"){
  dat=fread(infile,quote="")
  janitor::clean_names(dat)->dat
  as.numeric(dat$p_value) ->dat$p_value
  dat$confidence="low"
  dat[p_value <=1e-8,confidence:="high"]

  return(dat)

}


#' get_pheno Function to extract phenotype from omim string
#'
#' @param x
#'
#' @return
#' @export
#'
#' @examples
get_pheno<-function(x){
  # {Alkaline phosphatase, plasma level of, QTL 2}, 612367 (2)
  disease=TRUE
  if (grepl("\\[",x))
    disease=FALSE

  x=gsub(";.+","",x) #Take first entry

  m1=str_match(pattern="(.+),\\s*(\\d+)\\s+\\((\\d+)\\),*\\s*(.*)",string=x)

  phenotype=m1[2]

  mimid=m1[3]

  phenokey=m1[4]

  inheritance=m1[5]

  res=list(
    phenotype=phenotype,
    mimid=mimid,
    phenokey=phenokey ,
    inheritance=inheritance,
    disease=disease
  )
  return(res)
}