fromRevIsh {reb} | R Documentation |
This function will convert two lists of revish style strings to a matrix format.
fromRevIsh(enhList, dimList, chr, organism = "h")
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. |
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.
Karl J. Dykema, karl.dykema@vai.org Kyle A. Furge, kyle.furge@vai.org
MCR eset data was obtained with permission. See PMID: 15377468
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")