git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38548 bc3139a8-67e5-0310-9ffc-ced21a209358
Benilton Carvalho authored on 07/04/2009 11:22:53
| ... | ... |
@@ -109,3 +109,9 @@ is decoded and scanned |
| 109 | 109 |
2009-04-07 Rob Scharpf - committed version 1.0.73 |
| 110 | 110 |
|
| 111 | 111 |
* added cdfName as argument to computeCopynumber |
| 112 |
+ |
|
| 113 |
+2009-04-07 B Carvalho - committed versioni 1.0.74 |
|
| 114 |
+ |
|
| 115 |
+* Added documentation for snprma. |
|
| 116 |
+ |
|
| 117 |
+* Removed 'svn:executable' property of readIdatFiles.Rd |
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: crlmm |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays. |
| 4 |
-Version: 1.0.73 |
|
| 4 |
+Version: 1.0.74 |
|
| 5 | 5 |
Date: 2008-12-30 |
| 6 | 6 |
Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| 7 | 7 |
Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| 10 | 10 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,65 @@ |
| 1 |
+\name{snprma}
|
|
| 2 |
+\Rdversion{1.1}
|
|
| 3 |
+\alias{snprma}
|
|
| 4 |
+ |
|
| 5 |
+\title{
|
|
| 6 |
+ Preprocessing tool for SNP arrays. |
|
| 7 |
+} |
|
| 8 |
+\description{
|
|
| 9 |
+ SNPRMA will preprocess SNP chips. The preprocessing consists of |
|
| 10 |
+ quantile normalization to a known target distribution and |
|
| 11 |
+ summarization to the SNP-Allele level. |
|
| 12 |
+} |
|
| 13 |
+\usage{
|
|
| 14 |
+snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns) |
|
| 15 |
+} |
|
| 16 |
+\arguments{
|
|
| 17 |
+ \item{filenames}{
|
|
| 18 |
+ 'character' vector with file names. |
|
| 19 |
+} |
|
| 20 |
+ \item{mixtureSampleSize}{
|
|
| 21 |
+ Sample size to be use when fitting the mixture model. |
|
| 22 |
+} |
|
| 23 |
+ \item{fitMixture}{
|
|
| 24 |
+ 'logical'. Fit the mixture model? |
|
| 25 |
+} |
|
| 26 |
+ \item{eps}{
|
|
| 27 |
+ Stop criteria. |
|
| 28 |
+} |
|
| 29 |
+ \item{verbose}{
|
|
| 30 |
+ 'logical'. |
|
| 31 |
+} |
|
| 32 |
+ \item{seed}{
|
|
| 33 |
+ Seed to be used when sampling. |
|
| 34 |
+} |
|
| 35 |
+ \item{cdfName}{
|
|
| 36 |
+ cdfName: 'GenomeWideSnp_5', 'GenomeWideSnp_6' |
|
| 37 |
+} |
|
| 38 |
+ \item{sns}{
|
|
| 39 |
+ Sample names. |
|
| 40 |
+} |
|
| 41 |
+} |
|
| 42 |
+\value{
|
|
| 43 |
+ \item{A}{Summarized intensities for Allele A}
|
|
| 44 |
+ \item{B}{Summarized intensities for Allele B}
|
|
| 45 |
+ \item{sns}{Sample names}
|
|
| 46 |
+ \item{gns}{SNP names}
|
|
| 47 |
+ \item{SNR}{Signal-to-noise ratio}
|
|
| 48 |
+ \item{SKW}{Skewness}
|
|
| 49 |
+ \item{mixtureParams}{Parameters from mixture model}
|
|
| 50 |
+ \item{cdfName}{Name of the CDF}
|
|
| 51 |
+} |
|
| 52 |
+\examples{
|
|
| 53 |
+if (require(genomewidesnp5Crlmm) & require(hapmapsnp5)){
|
|
| 54 |
+ path <- system.file("celFiles", package="hapmapsnp5")
|
|
| 55 |
+ |
|
| 56 |
+ ## the filenames with full path... |
|
| 57 |
+ ## very useful when genotyping samples not in the working directory |
|
| 58 |
+ cels <- list.celfiles(path, full.names=TRUE) |
|
| 59 |
+ snprmaOutput <- snprma(cels) |
|
| 60 |
+ snprmaOutput[["A"]][1:10,] |
|
| 61 |
+ snprmaOutput[["B"]][1:10,] |
|
| 62 |
+} |
|
| 63 |
+} |
|
| 64 |
+\keyword{manip}
|
|
| 65 |
+\keyword{classif}
|