FormatSineOut {Oscope} | R Documentation |
Format SinFun outputs from lists to matrix
FormatSineOut(result, DataInSc, ShiftRg=pi/4)
result |
Output from SineFun |
DataInSc |
a gene-by-sample (isoform-by-sample) matrix indicating the rescaled expression of two genes/isoforms. all values should be bettwen [-1, 1]. |
ShiftRg |
phase shift cutoff. |
Output is a list with 4 sublists, each shows a N-by-N matrix, in which#' N is the total number of genes (isoforms). SimiMat: similarity matrix (sine scores); the sine scores are calculated by -log10(epsilon^2). DiffMat: dissimilarity matrix; shown are epsilon^2 for each gene pair. ShiftMat: optimal phase shift estimate for each pair of genes.
Ning Leng
aa <- sin(seq(0,1,.1)) bb <- sin(seq(0.5,1.5,.1)) cc <- sin(seq(0.9,1.9,.1)) DataInSc <- rbind(aa,bb,cc) NumGene <- nrow(DataInSc) Res <- sapply(1:(NumGene-1),function(i)SineFun(DataInSc, i),simplify=FALSE) Out <- FormatSineOut(Res, DataInSc)