snprma: Preprocessing tool for SNP arrays.
In crlmm: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Description Usage Arguments Details Value Examples

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

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snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns)
snprma2(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns)

`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.

'snprma2' allows one to genotype very large datasets (via ff package) and also permits the use of clusters or multiple cores (via snow package) to speed up preprocessing.

`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

if (require(genomewidesnp6Crlmm) & require(hapmapsnp6) & require(oligoClasses)){
  path <- system.file("celFiles", package="hapmapsnp6")

  ## 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,]
}
## Not run: 
## HPC Example
library(ff)
library(snow)
library(crlmm)
## genotype 50K SNPs at a time
ocProbesets(50000)
## setup cluster - 8 cores on the machine
setCluster(8, "SOCK")

path <- system.file("celFiles", package="hapmapsnp6")
cels <- list.celfiles(path, full.names=TRUE)
snprmaOutput <- snprma2(cels)


## End(Not run)