Convert from revish strings to a matrix

Description

This function will convert two lists of revish style strings to a matrix format.

Usage

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fromRevIsh(enhList, dimList, chr, organism = "h")

Arguments

enhList

list of enhanced bands on each individual sample

dimList

list of diminished bands on each individual sample

chr

chromosome to examine

organism

character, "h" for human, "m" for mouse, and "r" for rat.

Value

A matrix is returned. The rownames of this matrix correspond to the major bands located on that chromosome, and the columns correspond to the sample names.

Author(s)

Karl J. Dykema, karl.dykema@vai.org Kyle A. Furge, kyle.furge@vai.org

References

MCR eset data was obtained with permission. See PMID: 15377468

See Also

reb,revish

Examples

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mb.chr <- buildChromCytoband("h")

data(mcr.eset)
data(idiogramExample)
	## Create a vector with the index of normal samples
norms <- grep("MNC",colnames(mcr.eset@exprs))
	## Smooth the data using the default 'movbin' method, with the normal samples as reference and median centering
cset <- reb(mcr.eset@exprs,vai.chr,ref=norms,center=TRUE)
	## Mask the cset to remove noise
exprs <- cset[,-norms]
exprs[abs(exprs) < 1.96] <- NA
	## Extract the aberrations on the 5th chromosome
revish <- revish(exprs,vai.chr,"5")
	## Convert back to matrix
reconverted <- fromRevIsh(revish[[1]],revish[[2]],"5")


layout(cbind(1,2))
idiogram(cset[,-norms],vai.chr,"5",method="i",dlim=c(-2,2),col=.rwb,main="chr 5 reb results")
idiogram(reconverted,mb.chr,"5",method="i",dlim=c(-1,1),col=.rwb,main="chr 5 converted \n and re-converted")