snprma {crlmm}R Documentation

Preprocessing tool for SNP arrays.

Description

SNPRMA will preprocess SNP chips. The preprocessing consists of quantile normalization to a known target distribution and summarization to the SNP-Allele level.

Usage

snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns)

Arguments

filenames 'character' vector with file names.
mixtureSampleSize Sample size to be use when fitting the mixture model.
fitMixture 'logical'. Fit the mixture model?
eps Stop criteria.
verbose 'logical'.
seed Seed to be used when sampling.
cdfName cdfName: 'GenomeWideSnp_5', 'GenomeWideSnp_6'
sns Sample names.

Value

A Summarized intensities for Allele A
B Summarized intensities for Allele B
sns Sample names
gns SNP names
SNR Signal-to-noise ratio
SKW Skewness
mixtureParams Parameters from mixture model
cdfName Name of the CDF

Examples

if (require(genomewidesnp5Crlmm) & require(hapmapsnp5)){
  path <- system.file("celFiles", package="hapmapsnp5")

  ## the filenames with full path...
  ## very useful when genotyping samples not in the working directory
  cels <- list.celfiles(path, full.names=TRUE)
  snprmaOutput <- snprma(cels)
  snprmaOutput[["A"]][1:10,]
  snprmaOutput[["B"]][1:10,]
}

[Package crlmm version 1.2.4 Index]