normalizeNpData: Processes the non-polymorphic data

In cn.farms: cn.FARMS - factor analysis for copy number estimation

Description

Normalization for non-polymorphic data for Affymetrix SNP5 and SNP6

Usage

normalizeNpData(filenames, cores = 1, annotDir = NULL, runtype = "ff",
  saveFile = "npData", method = c("baseline", "quantiles", "none"))

Arguments

filenames	the absolute path of the CEL files as a list
cores	number of cores for used for parallelization
annotDir	Optional annotation directory.
runtype	Mode how the results are saved. Possible values are ff or bm. If ff is chosen the data will not be saved automatically. With bm the results will be saved permanently.
saveFile	Name of the file to save.
method	The method for the normalization.

Value

An instance of ExpressionSet containing the non-polymorphic data of the microarray.

Author(s)

Djork-Arne Clevert [e-mail] and Andreas Mitterecker [e-mail]

Examples

## Not run: 
library("hapmapsnp6")
celDir <- system.file("celFiles", package = "hapmapsnp6")
filenames <- dir(path = celDir, full.names = TRUE)
createAnnotation(filenames = filenames)
npData <- normalizeNpData(filenames)

## End(Not run)

cn.farms documentation built on Nov. 8, 2020, 7:59 p.m.