snprma: Preprocessing tool for SNP arrays.

In benilton/crlmm: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina 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)
snprma2(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.

Details

'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.

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(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)

benilton/crlmm documentation built on Dec. 27, 2019, 12:12 a.m.