Oscope (version 1.2.0)

PipeShiftCDF: Calculate residual of the sliding polynomial regression

Description

Calculate residual of the sliding polynomial regression

Usage

PipeShiftCDF(Data, Ndg=3, NChun=4, RdmStart=FALSE)

Arguments

Data

gene-by-sample matrix or isoform-by-sample matrix. It should be rescaled to values bwteen [-1,1].

Ndg

degree of polynomial.

NChun

number of starting points for polynomial fitting.

RdmStart

whether the start points are randomly selected.

Value

The function will fit sliding polynomial regression (SPR) to each row of the data. For each gene/isoform, SPR fits NChun polynomial curves with different starting points (samples). The samples with smaller order than the start point will be appended to follow the last sample when fitting. So each fitting consider same number of samples. If RdmStart = TRUE, the start points are randomly selected. Otherwise they are evenly sampled along the sample order. The aggregated MSE of a fit (using a specific start point) is defined as the summation of the MSEs of all genes/isoforms considered here. The output returns the MSE of the SPR, which is the largest aggregated MSE across fits using different start points.

Examples

aa <- sin(seq(0,1,.1))
bb <- sin(seq(0.5,1.5,.1))
cc <- sin(seq(0.9,1.9,.1))
res <- PipeShiftCDF(rbind(aa,bb,cc), NChun=2)