inst/scripts/Olink_qPCR.R

In pQTLdata: A Collection of Proteome Panels and Meta-Data

create_Olink_qPCR <- function()
{
  Lines <- 36
  INF <- Sys.getenv("INF")
  r <- readLines(paste(INF,"doc","Olink.R",sep='/'),n=Lines)
  write(r,file=paste(Lines))
  source(paste(Lines))
  unlink(paste(Lines))
  unlink("inf1.csv")
  unlink("inf2.csv")

  panels <- list()
  for(i in 1:length(tabs))
  {
    panel <- gsub(" |-", "_", tabs[i])
    target_uniprot <- get(panel)[1:2]
    names(target_uniprot) <- c("Target","UniProt")
    panels[[i]] <- data.frame(Panel=panel,target_uniprot)
  }
  p12 <- do.call(rbind,panels)

  library(biomaRt)

# hg19/GRCh37
# listMarts()
# listEnsemblArchives()
  hg19 <- useMart(biomart= "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host = "grch37.ensembl.org")
# listDatasets(hg19)
# listAttributes(hg19)
# listFilters(hg19)
  hg19.bm <- getBM(attributes = c('uniprotswissprot', 'hgnc_symbol','chromosome_name', 'start_position', 'end_position'),
                   filters = 'uniprotswissprot',
                   values = unique(with(p12,UniProt)),
                   mart = hg19)
  hg19.bed <- subset(hg19.bm,chromosome_name%in%c(1:22,'X','Y'))
  names(hg19.bed) <- c("UniProt","gene","chr","start","end")
  Olink_qPCR <- merge(p12,hg19.bed,by="UniProt",all=TRUE)
  save(Olink_qPCR,file='Olink_qPCR.rda',compress='xz')

  single_panel <- function()
    save(Cardiometabolic, 
         Cell_Regulation,
         CVD_II,
         CVD_III,
         Development,
         Immune_Response,
         Immuno_Oncology,
         Inflammation,
         Metabolism,
         Neurology,
         Oncology_II,
         Organ_Damage,
         file='Olink_qPCR_info.rda',compress='xz')
}