Nothing
getPSRnetaffxdatXTA <- function(arraytype, datafile,
pkgname, pkg.db, chip.pd, comparewithcdf = FALSE){
dat <- data.table::fread(datafile)
pt = data.table::data.table(probesetid = dat$probesetid,
symbol = dat$symbol,
ref_id = dat$ref_id,
db.symbol = dat$db.symbol,
db.name = dat$db.name,
chr = dat$chr,
start = dat$start,
stop = dat$stop,
nProbes = dat$nProbes,
locustype = dat$locustype,
probesettype = dat$probesettype,
stringsAsFactors = TRUE)
class(pt) = c("netaffx.db.annot", class(pt))
## assign
dataEnv = new.env(parent=emptyenv())
assign(pkgname, pt, envir=dataEnv)
datasource = paste("This package contains a detailed probesetid-level annotation file for use with the GCSscore R package. It was created by parsing annotation data from the 'netaffxProbeset.rda' data contained within the Bioconductor chip-type platform design (pd) package: ",chip.pd, "and from the Bioconductor transcriptclusterid-level annotation data (db) package: ",pkg.db,". This package was created using a customized version of the makeProbePackage function and a custom 'ProbePkg-template', both of which are sourced from the AnnotationForge package (version 1.28.0). These modificed files are contained in the GCSscore R package, which is available on Github and Bioconductor",sep="")
symVal = list(ARRAYTYPE = arraytype,
DATASOURCE = datasource,
NROW = as.character(nrow(pt)),
NCOL = as.character(ncol(pt)),
CHIP.PD = chip.pd,
PKG.DB = pkg.db)
return(list(pkgname = pkgname, symVal = symVal, dataEnv = dataEnv))
}
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