pdInfoBuilder (version 1.36.0)

makePdInfoPackage: Create a Platform Design Info Package

Description

This generic function create a platform design info package based on the parameters contained in object which will generally be an instance of a subclass of PkgSeed. The result is a new directory on the filesystem containing the source for the generated pdInfo package.

Usage

makePdInfoPackage(object, destDir, batch_size = 10000, quiet = FALSE, unlink = FALSE)

Arguments

object

See showMethods("makePdInfoPackage") to see available methods.

destDir

Path where the resulting pdInfo package source directory will be written.

batch_size

An integer controlling the size of batches processed when reading the flatfiles and loading the DB. In general, larger values of batch_size will use more memory and less time (unless you exceed physical memory, in which case more time will be used as well).

quiet

A logical value. When TRUE, diagnostic and status messages are not printed.

unlink

A logical value. If 'TRUE', and 'destDir' already contains a file or directory with the name 'pkgname', try to unlink (remove) it.

Value

This function is called for its side-effect of producing a pdInfo source package directory.

Details

In general, creating the SQLite database will be a time and memory intensive task.

Examples

cdfFile <- "Mapping250K_Nsp.cdf"
csvAnno <- "Mapping250K_Nsp_annot.csv"
csvSeq <- "Mapping250K_Nsp_probe_tab"

## Not run: 
# pkg <- new("AffySNPPDInfoPkgSeed",
#            version="0.1.5",
#            author="A.U. Thor", email="[e-mail]",
#            biocViews="AnnotationData",
#            genomebuild="NCBI Build 35, May 2004",
#            cdfFile=cdfFile, csvAnnoFile=csvAnno, csvSeqFile=csvSeq)
# 
# makePdInfoPackage(pkg, destDir=".")
# ## End(Not run)