inst/scripts/INTERVAL.R

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

sts <- function()
# INTERVAL SomaLogic results
{
  dir <- 'https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-018-0175-2/MediaObjects/'
  file <- '41586_2018_175_MOESM4_ESM.xlsx'
  xlsx <- paste0(dir,file)
  st4.1 <- openxlsx::read.xlsx(xlsx, sheet=4, colNames=TRUE, skipEmptyRows=TRUE,
                               cols=c(1:16,26:28), rows=c(5:1986))
  s t4.2 <- openxlsx::read.xlsx(xlsx, sheet=4, colNames=TRUE, skipEmptyRows=TRUE,
                              cols=c(17:25,29:31), rows=c(6:1986))
  st4 <- cbind(st4.1,st4.2)
  save(st4,file='st4.rda',compress='xz')
  st5 <- openxlsx::read.xlsx(xlsx, sheet=5, colNames=TRUE, skipEmptyRows=TRUE,
                             cols=c(1:19), rows=c(3:2746))
  st6.1 <- openxlsx::read.xlsx(xlsx, sheet=6, colNames=TRUE, skipEmptyRows=TRUE,
                             cols=c(1:11:13), rows=c(3:167))
  st6.2 <- openxlsx::read.xlsx(xlsx, sheet=6, colNames=TRUE, skipEmptyRows=TRUE,
                             cols=c(14:20), rows=c(4:167))
  st6 <- cbind(st6.1,st6.2)
  save(st6,file='st6.rda',compress='xz')
  replicates <- merge(st4[,c(1:12,26:28)],st6[,c(1:10,17:20)],
                      by=c("Locus.ID","UniProt","Chr","Pos","SOMAmer.ID"))
  line_to_edit <- with(replicates,Locus.ID=="3_59"|Locus.ID=="5_29")
  replicates[line_to_edit,"UniProt"] <- "P29460"

# However, it is unclear UniProts in ST6 were selected from which of the panels
  INF <- Sys.getenv("INF")
  INF1_merge <- merge(inf1,
                      read.delim(file.path(INF,"work","INF1.merge-rsid"),as.is=TRUE),
                      by="prot")
  INF1_uniprot <- unique(with(INF1_merge,uniprot))
  st6_replicates <- subset(replicates,UniProt %in% INF1_uniprot)
  table(subset(st6_replicates,UniProt %in% INF1_uniprot)$Replicates)

# side information on cvd2, cvd3, inf1
  olink <- scan(file.path(INF,"doc","olink.prot.list.txt"),"")
  olink_uniprot <- unlist(lapply(strsplit(olink,"___"),'[[',2))
  dim(subset(replicates,UniProt %in% olink_uniprot))

  z <- with(st6_replicates,{
    chr <- st6_replicates[["Chr"]]
    pos <- st6_replicates[["Pos"]]
    a1 <- st6_replicates[["Effect.Allele.(EA)"]]
    a2 <- st6_replicates[["Other.Allele.(OA)"]]
    cbind(UniProt,snpid=chr_pos_a1_a2(chr,pos,a1,a2))
  })

  doubles <- c("P29460","Q9NPF7","Q14213","Q8NEV9")
  subset(inf1,uniprot %in% doubles)
  write.table(merge(inf1,z,by.x="uniprot",by.y="UniProt")[c("snpid","prot","uniprot")],
              file="SomaLogic.id3",col.names=FALSE,row.names=FALSE,quote=FALSE)

  st18 <- openxlsx::readWorkbook(xlsx,sheet="ST18 - proteins assayed",startRow=3)
  save(st18,file='st18.rda',compress='xz')
  st20 <- openxlsx::read.xlsx(xlsx, sheet=20, colNames=TRUE, skipEmptyRows=TRUE,
                            cols=c(1:10), rows=c(3:786))
  ov <- intersect(unique(st20$UniProt),inf1$uniprot)
  ovv <- subset(st20,UniProt%in%ov)
  dim(ovv)
}