affyParaIntern {affyPara}R Documentation

Internal affyPara objects / functions

Description

Internal functions for the affyPara package.

Usage

initAffyBatchSF(object, object.type)

getAffyBatchSF()
getIntensitySF(rows, refindexname)
getCompIntensitySF(rows)
getCompIntensityMatrixSF(rows, drop=FALSE)
getFUNAffyBatchSF(FUN)

createDirSF(to, showWarnings = TRUE, recursive = TRUE)
writeLinesSF(data, fileName)
listFilesSF(path, full.names=TRUE)
ReadHeader(object)

file.name(file, fsep = .Platform$file.sep)

getObjectType(object)
checkPartSize(object, number.parts)

Arguments

object An object of class AffyBatch OR a character vector with the names of CEL files OR a (partitioned) list of character vectors with CEL file names.
object.type Declaration for the type of the argument object: "AffyBatch", "CELfileVec", "partCELfileList"
rows Number of rows which have to be changed.
refindexname The name of the array used as a reference.
drop A logical value. If TRUE the dimensions of an array which have only one level will be deleted.
FUN A function generating a value from a an AffyBatch. e.g. dim
to A character vector, that defines the path and name of the new directory.
showWarnings A logical value; should the warnings on failure be shown?
recursive A logical values; should elements of the path other than the last be created? If TRUE, like Unix's mkdir -p.
data A character vector, containing the data for the file.
fileName A character string with the file name.
path A character vector with the full directory.
full.names A logical value. If TRUE, the directory path is prepended to the file names. If FALSE, only the file names are returned.
file A character vector of file names with prepended directory path.
fsep A character string, giving the file separator used on your platform.
number.parts Number of nodes in the computer cluster.

Details

Internal functions for the affyPara package. The functions have to be used in a cluster function (e.g. clusterApply) from the SNOW package.

initAffyBatchSF
Slavefunction for initializing an AffyBatch at slaves. AffyBatch will be stored in the .GlobalEnv with the name 'AffyBatch'.
getAffyBatchSF
Slavefunction to get an AffyBatch from slaves. Gets the object AffyBatch from the .GlobalEnv.
getIntensitySF
Slavefunction to get special values from the intensity matrix from slaves.
getCompIntensitySF
Slavefunction to get special rows from the intensity matrix from slaves.
getCompIntensityMatrixSF
Slavefunction to get complete intensity matrix from slaves.
getFUNAffyBatchSF
Slavefunction to get a value from an AffyBatch at slaves.
createDirSF
Slavefunction to create a directory at slaves.
writeLinesSF
Slavefunction to write data into a file at slaves.
listFilesSF
Slavefunction to list files from directory at slaves.
ReadHeader
Slavefunction to return Header-Informations from CEL Files at slaves.
file.name
Function to get file name from a character with complete file path (directory path and filename).
getObjectType
Function to get type from object.
checkPartSize
Function to check object for length.

Author(s)

Markus Schmidberger schmidb@ibe.med.uni-muenchen.de, Ulrich Mansmann mansmann@ibe.med.uni-muenchen.de


[Package affyPara version 1.0.0 Index]