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]