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{correl2Comp} 

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+\alias{correl2Comp} 

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+\title{correl2Comp} 

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+\description{This function computes the correlation between two components.} 

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+\usage{correl2Comp(comp1, comp2, type.corr = "pearson", plot = FALSE, 

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+ cutoff_zval = 0, test = FALSE, alreadyTreat = FALSE)} 

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+\arguments{ 

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+ \item{comp1}{The first component, a vector of projections or contributions indexed by labels} 

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+ \item{comp2}{The second component, a vector of projections or contributions indexed by labels} 

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+ \item{type.corr}{Type of correlation to be computed, either \code{'pearson'} or \code{'spearman'}} 

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+ \item{plot}{if \code{TRUE}, plot \code{comp1} vs \code{comp2}} 

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+ \item{cutoff_zval}{either NULL or 0 (default) if all genes are used to compute the correlation between the components, or a threshold to compute the correlation on the genes that have at least a scaled projection higher than cutoff_zval. } 

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+ \item{test}{if TRUE the correlation test pvalue is returned instead of the correlation value} 

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+ \item{alreadyTreat}{if TRUE comp1 and comp2 are considered as being already treated (i.e scaled and restricted to common elements) } 

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+} 

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+\details{Before computing the correlation, the components are scaled and restricted to common labels. 

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+When \code{cutoff_zval} is different from \code{0}, the elements that are included in the circle of center 0 and radius \code{cutoff_zval} are not taken into account during the computation of the correlation.} 

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+\value{This function returns either the correlation value or the pvalue of the correlation test.} 

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+ 

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+\author{Anne Biton} 

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+ 

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+ 

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+ 

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+ 

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+ 