R/gene_symbol_converters.R

In effiken/scDissector: Exploratory Data Analysis tool for single-cell RNA-seq data

get_gene_symbol_conveters <- function(hgnc_file){
  hgnc<-read.delim(hgnc_file,header = T,stringsAsFactors = F)
  old_symbol=ifelse(hgnc[,"prev_symbol"]=="",hgnc[,"symbol"],hgnc[,"prev_symbol"])
  l_old_symbol=strsplit(old_symbol,"\\|")
  old_symbol2=unlist(l_old_symbol)

  new_symbol=hgnc[,"symbol"]
  new_symbol2=rep(new_symbol,sapply(l_old_symbol,length))

  gene_symbol_old2new<-new_symbol2
  names(gene_symbol_old2new)<-old_symbol2

  gene_symbol_new2old<-old_symbol
  names(gene_symbol_new2old)<-new_symbol
  return(list(old2new=gene_symbol_old2new,new2old=gene_symbol_new2old))
}

cap <- function(x) {
  paste(toupper(substring(x, 1,1)), tolower(substring(x, 2)),sep="", collapse=" ")
}

adjust_gene_names <- function(genes_string,data_genes){
  genes=strsplit(genes_string,",|, | ,")[[1]]
  mask1=toupper(genes)%in%data_genes
  genes[mask1]=toupper(genes[mask1])
  mask2=unlist(sapply(genes,cap))%in%data_genes
  genes[mask2]=unlist(sapply(genes[mask2],cap))
  mask3=gene_symbol_old2new[genes]%in%data_genes
  genes[mask3]=gene_symbol_old2new[genes[mask3]]
  mask4=gene_symbol_new2old[genes]%in%data_genes
  genes[mask4]=gene_symbol_new2old[genes[mask4]]
  genges=genes[!is.na(genes)]
  return(genes)

}

### gene symbol converters
load_gene_symbol_converters=function(){
    hgnc_file=system.file("extdata", "hgnc_complete_set.txt", package="scDissector")
    if (hgnc_file==""){
        hgnc_file="../extdata/hgnc_complete_set.txt"
    }
    hgnc<-read.delim(hgnc_file,header = T,stringsAsFactors = F)
    old_symbol=ifelse(hgnc[,"prev_symbol"]=="",hgnc[,"symbol"],hgnc[,"prev_symbol"])
    l_old_symbol=strsplit(old_symbol,"\\|")
    old_symbol2=unlist(l_old_symbol)
    
    new_symbol=hgnc[,"symbol"]
    new_symbol2=rep(new_symbol,sapply(l_old_symbol,length))
    
    gene_symbol_old2new<-(new_symbol2)
    names(gene_symbol_old2new)<-old_symbol2
    
    gene_symbol_new2old<-old_symbol
    names(gene_symbol_new2old)<-new_symbol
    return(list(old2new=gene_symbol_old2new,new2old=gene_symbol_new2old))
}