convert.output {snapCGH} | R Documentation |
This function converts the output obtained by applying our simulation scheme into a format that can be used (either directly or indirectly) as the input to various segmentation schemes available within R. Additionally, we are in the process of submitting a library to CRAN which will enable the user to apply a number of the segmentation schemes available within R to datasets which have the same structure as that generated by this function.
convert.output(input)
input |
The output obtained upon applying the sim.structure function |
This function outputs an object which is similar in structure/format to an RG or MA object used in Limma.
This function outputs a list with entries
M |
A matrix continaing the $mbox{log}_2$ ratios |
genes |
A matrix containing the simulated midpoints and the chromosome which forms the template upon which the simulation is based. |
Michael Smith, John Marioni
## The function is currently defined as function(input){ holder <- list() for (i in 1:length(input)){ holder[[i]] <- list()} for(i in 1:length(input)){ holder[[i]]$genes <- matrix(NA, nrow = length(input[[i]]$clones$mid.point), ncol = 2) } for(i in 1:length(input)){ holder[[i]]$M <- as.matrix(input[[i]]$datamatrix) holder[[i]]$genes[,1] <- input[[i]]$clones$mid.point holder[[i]]$genes[,2] <- rep(input[[i]]$chrom,length(input[[i]]$clones$mid.point)) colnames(holder[[i]]$genes) <- c("kb", "Chrom") holder[[i]] <- new("aCGHList", holder[[i]]) } holder }