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Question: Eisen-formatted expression data
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gravatar for Steffen Moeller
13.4 years ago by
Steffen Moeller40 wrote:
Below I paste a function that reads expression data from files formatted for Michael Eisen's Cluster tool. If somebody took this (code/idea) and incorporated it into the core of BioConductor, I would very much appreciate it. A write.eisen function might be very helpful, too. Is this of interest, should I go ahead? Where in BioConductor would this fit in? Kind regards Steffen # Reads microarray expression data formatted for # Michael Eisen's Cluster tool. # by Steffen Moeller <moeller@pzr.uni-rostock.de> read.eisen <- function(file,sep="\t",dec=".") { f<-read.table(file=file,header=TRUE,sep=sep,dec=dec) rownames(f)<-f[,1] if ("UNIQID"!=colnames(f)[1]) { stop(paste("This is not a proper Eisen-formatted file ('",file,"').",sep="")) } if ("NAME"==colnames(f)[2]) { colstart<-3 } else { colstart<-2 } if (""==rownames(f)[1]) { rowstart<-2 } else { rowstart<-1 } r<-f[rowstart:nrow(f),colstart:ncol(f)] if (2==rowstart) { attr(r,"second.row")<-f[1,colstart:ncol(f)] } else { attr(r,"second.row")<-NULL } if (3==colstart) { attr(r,"NAME")<-f[rowstart:nrow(f),2] } else { attr(r,"NAME")<-NULL } return(r) }
ADD COMMENTlink modified 13.4 years ago by Sean Davis21k • written 13.4 years ago by Steffen Moeller40
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gravatar for Sean Davis
13.4 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Apr 12, 2005, at 6:10 AM, Steffen Moeller wrote: > Below I paste a function that reads expression data from files > formatted > for Michael Eisen's Cluster tool. If somebody took this (code/idea) and > incorporated it into the core of BioConductor, I would very much > appreciate it. A write.eisen function might be very helpful, too. Is > this of interest, should I go ahead? Where in BioConductor would this > fit in? Have you looked at the ctc package? Looks like it has at least some of that functionality. http://www.bioconductor.org/repository/devel/package/html/ctc.html Sean
ADD COMMENTlink written 13.4 years ago by Sean Davis21k
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