snprma: Preprocessing tool for SNP arrays.

Description Usage Arguments Details Value Examples

View source: R/snprma-functions.R

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

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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)

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

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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.