frma (version 1.24.0)

makeVectorPackage: makeVectorPackage

Description

Make a package containing the vectors used by the frma package. If you don't plan to distribute and maintain this set of vectors, consider using either makeVectorsAffyBatch or makeVectorsFeatureSet instead.

Usage

makeVectorPackage(files, batch.id, version, maintainer, species, annotation, packageName, background="rma", normalize="quantile", normVec=NULL, type="AffyBatch", file.dir=".", output.dir=".", unlink=TRUE, verbose=TRUE)
  makeVectorsAffyBatch(files, batch.id, background="rma", normalize="quantile", normVec=NULL, cdfname=NULL, file.dir=".", verbose=TRUE)
  makeVectorsFeatureSet(files, batch.id, pkgname, background="rma", normalize="quantile", normVec=NULL, file.dir=".", verbose=TRUE)

Arguments

files

the CEL file names from which to create the vectors

batch.id

a vector of batch ids used to compute within and between batch variances

background

type of background correction to perform: either "none" or "rma".

normalize

type of normalization to perform: either "none" or "quantile".

normVec

normalization vector. If NULL, a normalization vector is created based on the given CEL files. Ignored if normalize is "none".

annotation

the "cdfname" or "pkgname" to be passed to either makeVectorsAffyBatch or makeVectorsFeatureSet depending on the value of "type".

cdfname

used to specify the name of an alternative cdf package. Passed to the ReadAffy function. If set to "NULL", then the usual cdf package based on Affymetrix's mappings will be used.

pkgname

alternative data package to be loaded. Passed to the read.celfiles function. If set to "NULL", then the default package will be used.

packageName

name of the package to be created

version

the version number of the package to be created

maintainer

typically your name

species

species of samples in object

type

the type of data object to be loaded. Must be one of: AffyBatch, FeatureSet.

file.dir

directory in which the CEL files are located

output.dir

directory in which to create the package

unlink

logical value. If TRUE and output.dir already contains a file or directory with the same name as the package being generated, then try to unlink (remove) it.

verbose

logical value. If TRUE then some messages are displayed while the function runs

Value

• The makeVectorPackage function creates a package with the name frmavecs. For example if the files are HGU133a arrays, the package would be called hgu133afrmavecs.

  The makeVectors functions create a list with 6 elements: ll{ normVec normalization vector probeVec probe effect vector probeVarWithin within batch probe variance probeVarBetween between batch probe variance probesetSD within probeset standard deviation medianSE median standard errors }

Examples

## assuming the celfiledir points to a directory with 9 CEL files
## this takes a long time
vecs <- makeVectorsAffyBatch(celfiledir, batch.id=rep(1:3, each=3))