## FIXME: we should offer to determine packageName based on header of
## CDF file and oligo::cleanPlatformName.
setMethod("makePdInfoPackage", "AffySNPPDInfoPkgSeed",
function(object, destDir=".", batch_size=10000, quiet=FALSE, unlink=FALSE) {
validInput <- function(x, destPath) {
msg <- NULL
ok <- sapply(c("cdfFile", "csvAnnoFile", "csvSeqFile"),
function(slt) file.exists(slot(x, slt)))
if (!all(ok))
msg <-
paste("missing file(s):",
paste(sapply(names(ok[!ok]), function(slt) slt),
"='",
sapply(names(ok[!ok]),
function(slt) slot(x, slt)),
"'",
collapse=", ", sep=""))
if (file.exists(destPath))
msg <-
c(msg,
paste("destination exists, remove or rename: '",
destPath, "'", sep=""))
if (is.null(msg)) TRUE else msg
}
chip <- chipName(object)
pkgName <- cleanPlatformName(chip)
valid <- validInput(object, file.path(destDir, pkgName))
if (!identical(valid, TRUE))
stop(paste(valid, collapse="\n "))
extdataDir <- file.path(destDir, pkgName, "inst", "extdata")
dbFileName <- paste(pkgName, "sqlite", sep=".")
dbFilePath <- file.path(extdataDir, dbFileName)
seqMatFile <- file.path(extdataDir, "seqMat.rda")
geometry <- paste(readCdfHeader(object@cdfFile)[c("nrows", "ncols")], collapse=";")
syms <- list(MANUF=object@manufacturer,
VERSION=object@version,
GENOMEBUILD=object@genomebuild,
AUTHOR=object@author,
AUTHOREMAIL=object@email,
LIC=object@license,
DBFILE=dbFileName,
CHIPNAME=chip,
PKGNAME=pkgName,
PDINFONAME=pkgName,
PDINFOCLASS="AffySNPPDInfo",
GEOMETRY=geometry)
templateDir <- system.file("pd.PKG.template2",
package="pdInfoBuilder")
createPackage(pkgname=pkgName, destinationDir=destDir,
originDir=templateDir, symbolValues=syms,
# getting error on invalid use of ..., vjc 5 jul 2007
# quiet=quiet, ...)
quiet=quiet)
dir.create(extdataDir, recursive=TRUE)
buildPdInfoDb(object@cdfFile, object@csvAnnoFile,
object@csvSeqFile, dbFilePath, seqMatFile,
batch_size=batch_size, verbose=!quiet)
## copy external resource files
extFiles <- c(object@splineParamFile,
object@crlmmInfoFile,
object@referenceDistFile)
for (ef in extFiles) {
if (nchar(ef) > 0)
file.copy(ef, extdataDir)
}
})
setMethod("makePdInfoPackage", "AffySNPCNVPDInfoPkgSeed",
function(object, destDir=".", batch_size=1000, quiet=FALSE, unlink=FALSE) {
chip <- chipName(object)
pkgName <- cleanPlatformName(chip)
extdataDir <- file.path(destDir, pkgName, "inst", "extdata")
dbFileName <- paste(pkgName, "sqlite", sep=".")
dbFilePath <- file.path(extdataDir, dbFileName)
seqMatFile <- file.path(extdataDir, "seqMat.rda")
seqMatFileCnv <- file.path(extdataDir, "seqMatCNV.rda")
geometry <- paste(readCdfHeader(object@cdfFile)[c("nrows", "ncols")], collapse=";")
syms <- list(MANUF=object@manufacturer,
VERSION=object@version,
GENOMEBUILD=object@genomebuild,
AUTHOR=object@author,
AUTHOREMAIL=object@email,
LIC=object@license,
DBFILE=dbFileName,
CHIPNAME=chip,
PKGNAME=pkgName,
PDINFONAME=pkgName,
PDINFOCLASS="AffySNPCNVPDInfo",
GEOMETRY=geometry)
templateDir <- system.file("pd.PKG.template2",
package="pdInfoBuilder")
createPackage(pkgname=pkgName, destinationDir=destDir,
originDir=templateDir, symbolValues=syms,
quiet=quiet)
dir.create(extdataDir, recursive=TRUE)
snp6.buildPdInfoDb(object@cdfFile, object@csvAnnoFile,
object@csvSeqFile, object@csvAnnoFileCnv,
object@csvSeqFileCnv, dbFilePath, seqMatFile, seqMatFileCnv,
batch_size=batch_size, verbose=!quiet)
## copy external resource files
extFiles <- c(object@splineParamFile,
object@crlmmInfoFile,
object@referenceDistFile)
for (ef in extFiles) {
if (nchar(ef) > 0)
file.copy(ef, extdataDir)
}
})
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