Add Rd files for calculatePosteriorMean, genotypes, posteriorProbability, and predictionRegion

 ... ... @@ -1,7 +1,7 @@ 1 1  Package: crlmm 2 2  Type: Package 3 3  Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. 4 -Version: 1.11.10 4 +Version: 1.11.11 5 5  Date: 2010-12-10 6 6  Author: Benilton S Carvalho , Robert Scharpf , Matt Ritchie , Ingo Ruczinski , Rafael A Irizarry 7 7  Maintainer: Benilton S Carvalho , Robert Scharpf , Matt Ritchie
 8 8 new file mode 100644 ... ... @@ -0,0 +1,56 @@ 1 +\name{calculatePosteriorMean} 2 +\alias{calculatePosteriorMean} 3 +\alias{calculatePosteriorMean,CNSet-method} 4 +%- Also NEED an '\alias' for EACH other topic documented here. 5 +\title{Calculate the posterior mean of the integer copy numbers} 6 +\description{ 7 + 8 + Computes the posterior mean copy number from the bivariate normal 9 + prediction regions. 10 + 11 +} 12 + 13 +\usage{ 14 +calculatePosteriorMean(object, posteriorProb, copyNumber = 0:4, w, ...) 15 +} 16 +%- maybe also 'usage' for other objects documented here. 17 +\arguments{ 18 + \item{object}{ 19 + A \code{CNSet} object. 20 +} 21 + \item{posteriorProb}{ 22 + The posterior probability for copy numbers 0-4. 23 + } 24 + 25 + \item{copyNumber}{ 26 + Integer vector. 27 +} 28 +\item{w}{ 29 + The prior probability for the copy numbers in \code{copyNumber} 30 +} 31 + \item{\dots}{ 32 + Ignored 33 +} 34 +} 35 +\details{ 36 +} 37 +\value{ 38 + An array (features x samples x copy number) 39 +} 40 + 41 +\author{ 42 +R. Scharpf 43 +} 44 + 45 + 46 +%% ~Make other sections like Warning with \section{Warning }{....} ~ 47 + 48 +\seealso{ 49 + \code{\link{predictionRegion}}, \code{\link{posteriorProbability}} 50 +} 51 +\examples{ 52 +} 53 +% Add one or more standard keywords, see file 'KEYWORDS' in the 54 +% R documentation directory. 55 +\keyword{array} 56 +\keyword{models}
 0 57 new file mode 100644 ... ... @@ -0,0 +1,37 @@ 1 +\name{genotypes} 2 +\alias{genotypes} 3 +%- Also NEED an '\alias' for EACH other topic documented here. 4 +\title{ 5 + The possible genotypes for an integer copy number. 6 +} 7 +\description{ 8 + The possible genotypes for an integer copy number (0-4). 9 +} 10 +\usage{ 11 +genotypes(copyNumber) 12 +} 13 +%- maybe also 'usage' for other objects documented here. 14 +\arguments{ 15 + \item{copyNumber}{ 16 + Integer (0-4 allowed). 17 +} 18 +} 19 +\details{ 20 + 21 +} 22 +\value{ 23 + Character vector. 24 +} 25 + 26 +\author{ 27 +R. Scharpf 28 +} 29 + 30 + 31 +\examples{ 32 +for(i in 0:4) print(genotypes(i)) 33 +} 34 +% Add one or more standard keywords, see file 'KEYWORDS' in the 35 +% R documentation directory. 36 +\keyword{manip} 37 +x
 0 38 new file mode 100644 ... ... @@ -0,0 +1,51 @@ 1 +\name{posteriorProbability} 2 +\alias{posteriorProbability} 3 +\alias{posteriorProbability,CNSet-method} 4 +%- Also NEED an '\alias' for EACH other topic documented here. 5 +\title{Calculate the posterior probability for integer copy numbers.} 6 + 7 +\description{ 8 + Calculate the posterior probability for integer copy numbers using the 9 + bivariate normal prediction regions. 10 +} 11 + 12 +\usage{ 13 +posteriorProbability(object, predictRegion, copyNumber = 0:4) 14 +} 15 +%- maybe also 'usage' for other objects documented here. 16 +\arguments{ 17 + \item{object}{ 18 + A \code{CNSet} object. 19 +} 20 + \item{predictRegion}{ 21 + A list containing the bivariate normal prediction region for each of 22 + the possible genotypes. 23 +} 24 + \item{copyNumber}{ 25 + Integer vector. 26 +} 27 +} 28 +\details{ 29 + 30 +} 31 +\value{ 32 +An array (features x samples x copy number) 33 +} 34 + 35 +\author{ 36 +R. Scharpf 37 +} 38 +\note{ 39 + %Remark about nonpolymorphic probes 40 +} 41 + 42 +%% ~Make other sections like Warning with \section{Warning }{....} ~ 43 + 44 +\seealso{ 45 + \code{\link{predictionRegion}}, \code{\link{genotypes}}, \code{\link{calculatePosteriorMean}} 46 +} 47 +\examples{ 48 +} 49 +% Add one or more standard keywords, see file 'KEYWORDS' in the 50 +% R documentation directory. 51 +\keyword{array} 0 52 \ No newline at end of file
 1 53 new file mode 100644 ... ... @@ -0,0 +1,66 @@ 1 +\name{predictionRegion} 2 +\alias{predictionRegion} 3 +\alias{predictionRegion,CNSet,integer-method} 4 +\title{Prediction regions for integer copy number} 5 +\description{Bivariate normal prediction regions for integer copy 6 + number. Copy numbers 0-4 allowed.} 7 +\usage{ 8 +predictionRegion(object, copyNumber) 9 +} 10 +%- maybe also 'usage' for other objects documented here. 11 +\arguments{ 12 + \item{object}{A \code{CNSet} object.} 13 + \item{copyNumber}{Integer vector. 0-4 allowed.} 14 +} 15 +\details{ 16 + 17 + We fit a linear regression for each allele to the diallic genotype 18 + cluster medians. Denoting the background and slope by nu and phi, 19 + respectively, the mean for the bivariate normal prediction region is 20 + given by 21 + 22 + mu_A = nu_A + CA * phi_A 23 + 24 + and 25 + 26 + mu_B nu_B + CB * phi_B 27 + 28 + The variance and correlation of the normalized intensities is 29 + estimated from the diallelic genotype clusters AA, AB, and BB on the 30 + log-scale. For copy number not equal to two, we assume that the 31 + variance is approximately the same for copy number not equal to 2. 32 + 33 +} 34 + 35 +\value{ 36 + 37 + A list named by the genotype. NULL' refers to copy number zero, A' 38 + is a hemizygous deletion, etc. Each element is a list of the means 39 + (mu) and covariance (cov) for each marker. The covariance for each 40 + marker is stored as a vector in the order variance A, correlation, 41 + variance B. For nonpolymorphic markers, only the first mu and the 42 + first variance are used. 43 + 44 +} 45 + 46 + 47 +\references{ 48 + Scharpf et al., 2011, Biostatistics. 49 +} 50 +\author{ 51 + R. Scharpf 52 +} 53 + 54 +%% ~Make other sections like Warning with \section{Warning }{....} ~ 55 + 56 +\seealso{ 57 + 58 +} 59 +\examples{ 60 +data(sample.CNSet) 61 +pr <- predictionRegion(cnSet, copyNumber=0:4) 62 +} 63 +% Add one or more standard keywords, see file 'KEYWORDS' in the 64 +% R documentation directory. 65 +\keyword{ ~kwd1 } 66 +\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line