R/netaffxAnnotBuilderXTA.R

In harrisgm/GCSscore: GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

# Function to generate 'netaffx' annotations from platform 
# design (pd) packages from BioConductor.  The generated probeFile is stored 
# in a data.table within an .rda file. These annotations are then converted 
# to a custom 'probePackage' using the makeProbePacage() function from
# the AnnotationForge package.

# This function is for use on ClariomD/XTA Affymetrix arrays.

# Examples using platform design packages on Bioconductor, found at:
# https://www.bioconductor.org/packages/release/data/annotation/

netaffxAnnotBuilderXTA <- function(chip.pd = NULL, clean.chip = NULL, species.pd = NULL, packageName = NULL, annotName = NULL) {
  # Install necessary pd.* package if not already installed:
  # 03.02.20: is install.pd should not be needed in the function as it is
  # already in the GCSscore.R function
  # if (!requireNamespace(chip.pd, quietly = TRUE)){
  #   BiocManager::install(chip.pd)
  #   message("installing necessary platform design (pd) package from Bioconductor")}
  # 
  
  # get chip name (without periods/dots) from chip.pd:
  # clean.chip <- stringr::str_remove_all(strsplit(chip.pd,"pd.")[[1]][2],"[.]")
  # 03.02.20: the above line seems redundant, since clean.chip is the same thing (I think)
  
  # try the following conditional:
  if (packageName %like% "transcriptcluster"){
    message("Building full transcriptclusterid-based annotation file from Bioconductor sources")
    load(system.file("extdata","netaffxTranscript.rda",package = chip.pd))
    netaffx.TCid.all <- data.table(netaffxTranscript@data)
    
    netaffx.TCid.annot <- netaffx.TCid.all[,c("transcriptclusterid")]
    netaffx.TCid.annot[,symbol := sapply(strsplit(netaffx.TCid.all$geneassignment, " // "), "[", 2)]
    netaffx.TCid.annot[,ref_id := sapply(strsplit(netaffx.TCid.all$mrnaassignment, " // "), "[", 1)]
    netaffx.TCid.annot[,name := sapply(strsplit(netaffx.TCid.all$geneassignment, " // "), "[", 3)]
    netaffx.TCid.annot[,chr := sapply(strsplit(netaffx.TCid.all$seqname, " // "), "[", 1)]
    netaffx.TCid.annot[,start := netaffx.TCid.all$start]
    netaffx.TCid.annot[,stop := netaffx.TCid.all$stop]
    netaffx.TCid.annot[,nProbes := netaffx.TCid.all$totalprobes]
    netaffx.TCid.annot[,locustype := sapply(strsplit(netaffx.TCid.all$locustype, "///"), "[", 1 )]
    netaffx.TCid.annot[,category := netaffx.TCid.all$category]
    
    # Now intergrate the well-annotated symbols/names for the respective .db package:
    db.symbol <- eval(parse(text= paste("as.data.table(",packageName,"::",annotName,"SYMBOL)",sep = "")))
    db.genename <- eval(parse(text= paste("as.data.table(",packageName,"::",annotName,"GENENAME)",sep = "")))
    # set keys to 'probe_id' and merge the two annotations together:
    setkey(db.symbol,probe_id)
    setkey(db.genename,probe_id)
    db.TCid.annot <- db.symbol[db.genename]
    # rename columns to db.sybmol and db.name:
    names(db.TCid.annot) <- c("transcriptclusterid","db.symbol","db.name")
    # reset the keys:
    setkey(db.TCid.annot,transcriptclusterid)
    setkey(netaffx.TCid.annot,transcriptclusterid)
    netaffx.db.annot <- db.TCid.annot[netaffx.TCid.annot]
    # outdir <- "~/Desktop/"
    # merge them into a new data.table:
    
    outdir <- tempdir()
    # outdir <- "~/Desktop"
    
    netaffx.annot.tab <- paste(clean.chip,".netaffx.annot.probe_tab",sep="")
    netaffx.annot.loc <- paste(outdir,"/",netaffx.annot.tab,sep="")
    fwrite(netaffx.db.annot,file=netaffx.annot.loc,sep = "\t")
    annot.pkg.name = paste(clean.chip,".TC.netaffx.annot",sep="")
    

    makeAnnotPackageGCSs(
      arraytype = clean.chip,
      outdir = outdir,
      species = species.pd,
      chip.pd = chip.pd,
      maintainer= "Guy Harris <harrisgm@vcu.edu>",
      version = "0.0.5",
      pkgname = annot.pkg.name,
      pkg.db = packageName,
      datafile = netaffx.annot.loc,
      importfun = "getTCnetaffxdatXTA",
      check = FALSE)
    
    
    message("This transcriptcluster/TCid annotation package contains data parsed from the following source: ")
    message(paste("  (1) The nettaffx annotations from BioConductor platform design (pd) package: ",chip.pd,sep=""))
    message(paste("  (2) The concise list of well annotated genes from BioConductor annotation data (.db) package: ", packageName,sep=""))
    message(paste("transcriptcluster/TCid annotation package installing for chip: ",clean.chip,sep=""))

    pkg.loc <- paste(outdir,"/",annot.pkg.name,sep="")
    devtools::install(pkg = pkg.loc,upgrade = "never")
  }
  
  
  else if (packageName %like% "probeset"){
    message("Buidling full PSR/robesetid annotation file from netaffx and .db sources on Bioconductor")
    load(system.file("extdata","netaffxProbeset.rda",package = chip.pd))
    # Code below written and checked for all XTA arrays in: netAffx_annotation_builder_fullannot.R
    netaffx.PSR.all <- data.table(netaffxProbeset@data)
    netaffx.PSR.annot <- netaffx.PSR.all[,c("probesetid")]
    netaffx.PSR.annot[,symbol := sapply(strsplit(netaffx.PSR.all$geneassignment, "// | ///"), "[", 2)]
    netaffx.PSR.annot[,ref_id := sapply(strsplit(netaffx.PSR.all$mrnaassignment, " // "), "[", 1)]
    netaffx.PSR.annot[,chr := sapply(strsplit(netaffx.PSR.all$seqname, " // "), "[", 1)]
    netaffx.PSR.annot[,start := netaffx.PSR.all$start]
    netaffx.PSR.annot[,stop := netaffx.PSR.all$stop]
    netaffx.PSR.annot[,nProbes := netaffx.PSR.all$probecount]
    netaffx.PSR.annot[,locustype := sapply(strsplit(netaffx.PSR.all$locustype, "///"), "[", 1 )]
    netaffx.PSR.annot[,probesettype := netaffx.PSR.all$probesettype]
    
    # Now intergrate the well-annotated symbols/names for the respective .db package:
    db.symbol <- eval(parse(text= paste("as.data.table(",packageName,"::",annotName,"SYMBOL)",sep = "")))
    db.genename <- eval(parse(text= paste("as.data.table(",packageName,"::",annotName,"GENENAME)",sep = "")))
    # set keys to 'probe_id' and merge the two annotations together:
    setkey(db.symbol,probe_id)
    setkey(db.genename,probe_id)
    db.PSR.annot <- db.symbol[db.genename]
    # rename columns to db.sybmol and db.name:
    names(db.PSR.annot) <- c("probesetid","db.symbol","db.name")
    # reset the keys:
    setkey(db.PSR.annot,probesetid)
    setkey(netaffx.PSR.annot,probesetid)
    netaffx.db.annot <- db.PSR.annot[netaffx.PSR.annot]
    # outdir <- "~/Desktop/"
    # merge them into a new data.table:
    
    outdir <- tempdir()
    # datafile <- paste(chip,".netaffx.TCid.annot.tab",sep="")
    netaffx.annot.tab <- paste(clean.chip,".netaffx.annot.probe_tab",sep="")
    netaffx.annot.loc <- paste(outdir,"/",netaffx.annot.tab,sep="")
    fwrite(netaffx.db.annot,file=netaffx.annot.loc,sep = "\t")
    annot.pkg.name = paste(clean.chip,".PSR.netaffx.annot",sep="")


    makeAnnotPackageGCSs(
      arraytype = clean.chip,
      outdir = outdir,
      species = species.pd,
      chip.pd = chip.pd,
      maintainer= "Guy Harris <harrisgm@vcu.edu>",
      version = "0.0.5",
      pkgname = annot.pkg.name,
      pkg.db = packageName,
      datafile = netaffx.annot.loc,
      importfun = "getPSRnetaffxdatXTA",
      check = FALSE)
    
    
    
    message("This probesestid/PSR annotation package contains data parsed from the following source: ")
    message(paste("  (1) The nettaffx annotations from BioConductor platform design (pd) package: ",chip.pd,sep=""))
    message(paste("  (2) The concise list of well annotated genes from BioConductor annotation data (.db) package: ", packageName,sep=""))
    message(paste("probesestid/PSR annotation package installing for chip: ",clean.chip,sep=""))
    
    pkg.loc <- paste(outdir,"/",annot.pkg.name,sep="")
    devtools::install(pkg = pkg.loc,upgrade = "never")
    
  }else {message("netaffx data not available for chip type. Please recheck that the chip type is XTA before continuing")}
  
  return(message("DONE"))	
}

# Figuring out probepackages ----------------------------------------------
# 
# createRes <- createPackage(pkgname,
#                            destinationDir = outdir,
#                            originDir = system.file("ProbePkg-template", package=thispkg),
#                            symbolValues = symbolValues,
#                            unlink = F, quiet = F)