R/create_org_data.R

In jmzeng1314/biotrainee: Offer study material for fans in biotrainee

# rm(list=ls())
## firstly create gene information for human
if(F){
  library(org.Hs.eg.db)
  eg2symbol=toTable(org.Hs.egSYMBOL)
  eg2name=toTable(org.Hs.egGENENAME)
  eg2alias=toTable(org.Hs.egALIAS2EG)
  eg2alis_list=lapply(split(eg2alias,eg2alias$gene_id),function(x){paste0(x[,2],collapse = ";")})
  GeneList=mappedLkeys(org.Hs.egSYMBOL)
  if( GeneList[1] %in% eg2symbol$symbol ){
    symbols=GeneList
    geneIds=eg2symbol[match(symbols,eg2symbol$symbol),'gene_id']
  }else{
    geneIds=GeneList
    symbols=eg2symbol[match(geneIds,eg2symbol$gene_id),'symbol']
  }
  geneNames=eg2name[match(geneIds,eg2name$gene_id),'gene_name']
  geneAlias=sapply(geneIds,function(x){ifelse(is.null(eg2alis_list[[x]]),"no_alias",eg2alis_list[[x]])})

  human_gene_info_org=data.frame(   symbols=symbols,
                                    geneIds=geneIds,
                                    geneNames=geneNames,
                                    geneAlias=geneAlias,
                                    stringsAsFactors = F
  )
  devtools::use_data(human_gene_info_org, overwrite = T)

}
## Then create gene information for mouse
if(F){
  rm(list = ls())
  library(org.Mm.eg.db)
  eg2symbol=toTable(org.Mm.egSYMBOL)
  eg2name=toTable(org.Mm.egGENENAME)
  eg2alias=toTable(org.Mm.egALIAS2EG)
  eg2alis_list=lapply(split(eg2alias,eg2alias$gene_id),function(x){paste0(x[,2],collapse = ";")})
  GeneList=mappedLkeys(org.Mm.egSYMBOL)
  if( GeneList[1] %in% eg2symbol$symbol ){
    symbols=GeneList
    geneIds=eg2symbol[match(symbols,eg2symbol$symbol),'gene_id']
  }else{
    geneIds=GeneList
    symbols=eg2symbol[match(geneIds,eg2symbol$gene_id),'symbol']
  }
  geneNames=eg2name[match(geneIds,eg2name$gene_id),'gene_name']
  geneAlias=sapply(geneIds,function(x){ifelse(is.null(eg2alis_list[[x]]),"no_alias",eg2alis_list[[x]])})

  mouse_gene_info_org=data.frame(   symbols=symbols,
                                    geneIds=geneIds,
                                    geneNames=geneNames,
                                    geneAlias=geneAlias,
                                    stringsAsFactors = F
  )
  head(mouse_gene_info_org)
  devtools::use_data(mouse_gene_info_org, overwrite = T)

}

if(F){

  createLink <- function(base,val) {
    sprintf('<a href="%s" class="btn btn-link" target="_blank" >%s</a>',base,val) ##target="_blank"
  }
  gene_info=data.frame(   symbols=symbols,
                          geneIds=createLink(paste0("http://www.ncbi.nlm.nih.gov/gene/",geneIds),geneIds),
                          geneNames=geneNames,
                          geneAlias=geneAlias,
                          stringsAsFactors = F
  )
  #library("xtable")
  #print(xtable(gene_info), type="html",include.rownames=F, file='all_gene.anno',sanitize.text.function = force)
  file='all_gene_bioconductor.html'
  y <- DT::datatable(gene_info,escape = F,rownames=F)
  DT::saveWidget(y,file)

}