Oscope (version 1.2.0)

OscopeSine: Apply sine model on the full set of genes or isoforms

Description

Apply sine model on the full set of genes or isoforms

Usage

OscopeSine(DataInSc, parallel=FALSE, parallelParam=NULL)

Arguments

DataInSc

a gene-by-sample (isoform-by-sample) matrix indicating the rescaled expression of two genes/isoforms. all values should be bettwen [-1, 1].

parallel

whether apply parallel computing. if it is TRUE, BiocParallel will be called.

parallelParam

a SnowParam object to specify the clusters. If it is NULL, the default will be set as SnowParam(workers = 5, type = "SOCK") remains unchanged for over NCThre iterations.

Value

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.

Examples

aa <- sin(seq(0,1,.1))
bb <- sin(seq(0.5,1.5,.1))
cc <- sin(seq(0.9,1.9,.1))
OscopeSine(rbind(aa,bb,cc))