gitsvnid: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@73179 bc3139a867e503109ffcced21a209358
Marc Carlson authored on 05/02/2013 22:15:531  1 
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+\name{readA} 

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+\alias{readA} 

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+\title{read A} 

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+\usage{ 

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+ readA(Afile, datfile, dat, annot = TRUE) 

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+} 

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+\arguments{ 

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+ \item{Afile}{The file which contains the matrix of sample 

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+ contributions. It must be a txt file where the separator 

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+ is \code{white space}, that is one or more spaces, tabs, 

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+ newlines or carriage returns} 

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+ 

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+ \item{datfile}{The file which contains the matrix (of 

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+ dimension features x samples) based on which the matrix A 

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+ was calculated} 

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+ 

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+ \item{dat}{The data based on which the matrix A was 

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+ calculated (features x samples)} 

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+ 

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+ \item{annot}{TRUE (default) if the Afile contains 

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+ rownames of matrix A, FALSE if the rownames has to be 

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+ extracted from dat} 

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+} 

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+\value{ 

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+ This function returns a matrix of dimension samples x 

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+ components with rownames filled with sample IDs. 

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+} 

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+\description{ 

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+ readA 

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+} 

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+\details{ 

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+ This function reads and annotates matrix A. 

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+ 

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+ The matrix dat must be the one on which the matrix A was 

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+ calculated. It is assumed that the number of components 

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+ is lower than the number of samples, the matrix will be 

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+ transposed to have dimension 'samples x components' 

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+ according to this assumption. If \code{annot} is FALSE, 

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+ colnames of dat are used to annotate rownames of A. 

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+} 

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+\author{ 

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+ Anne Biton 

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+} 

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+\keyword{internal} 

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+ 