fromRevIsh: Convert from revish strings to a matrix

In reb: Regional Expression Biases

Description

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

Usage

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, [e-mail] Kyle A. Furge, [e-mail]

References

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

See Also

reb,revish

Examples

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")


	

reb documentation built on April 28, 2020, 8:35 p.m.