SNPRMA will preprocess SNP chips. The preprocessing consists of
quantile normalization to a known target distribution and
summarization to the SNP-Allele level.
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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(crlmm)
Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: preprocessCore
Welcome to crlmm version 1.30.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/crlmm/snprma.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snprma
> ### Title: Preprocessing tool for SNP arrays.
> ### Aliases: snprma snprma2
> ### Keywords: manip classif
>
> ### ** 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,]
+ }
Loading required package: genomewidesnp6Crlmm
Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19.
Loading required package: hapmapsnp6
/-------------------------------------------
| SAMPLE HAPMAP SNP 6.0 |
|-------------------------------------------|
| Data obtained from http://www.hapmap.org |
| This package is meant to be used only for |
| demonstration of BioConductor packages. |
| Access http://www.hapmap.org for details. |
|-------------------------------------------|
| The contents of this package are provided |
| in good faith and the maintainer does not |
| warrant their accuracy. |
-------------------------------------------/
Loading annotations and mixture model parameters.
Processing 3 files.
| | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%
[,1] [,2] [,3]
[1,] 1510 1164 2235
[2,] 793 749 668
[3,] 3541 3997 3502
[4,] 1098 336 309
[5,] 350 276 386
[6,] 243 297 309
[7,] 784 999 846
[8,] 557 600 482
[9,] 775 664 400
[10,] 813 1422 1527
> ## Not run:
> ##D ## HPC Example
> ##D library(ff)
> ##D library(snow)
> ##D library(crlmm)
> ##D ## genotype 50K SNPs at a time
> ##D ocProbesets(50000)
> ##D ## setup cluster - 8 cores on the machine
> ##D setCluster(8, "SOCK")
> ##D
> ##D path <- system.file("celFiles", package="hapmapsnp6")
> ##D cels <- list.celfiles(path, full.names=TRUE)
> ##D snprmaOutput <- snprma2(cels)
> ##D
> ## End(Not run)
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.