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

In Oscope: Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq

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.

Author(s)

Ning Leng

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))

Oscope documentation built on Nov. 8, 2020, 7:12 p.m.