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)
    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)

[Package crlmm version 1.40.0 Index]