gene-by-sample matrix or isoform-by-sample matrix.It should be rescaled to values bwteen
[-1,1].
Seq
NULL or a vector indicates the sample order.
if specified, the samples will be first reordered by this vector.
NChun
number of starting points for polynomial fitting.
RdmStart
whether the start points are randomly selected.
Ndg
degree of polynomial.
Value
This function performs the extended nearest insertion (ENI).
The ENI algorithm searchs for the optimal sample order which minimizes the MSE of
sliding polynomial regression (SPR).
This function will call PipeShiftCDF() function, which fits
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 MSE of the SPR is defined as the largest aggregated MSE across fits
using different start points.
The output returns the optimal order which provides the smallest SPR MSE.
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))
res <- ImpShift(rbind(aa,bb,cc), NChun=2)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(Oscope)
Loading required package: EBSeq
Loading required package: blockmodeling
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
Loading required package: testthat
Loading required package: cluster
Loading required package: BiocParallel
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Oscope/ImpShift.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ImpShift
> ### Title: Search for the optimal sample order by using the Extended
> ### Nearest Insertion
> ### Aliases: ImpShift
>
> ### ** Examples
>
> aa <- sin(seq(0,1,.1))
> bb <- sin(seq(0.5,1.5,.1))
> cc <- sin(seq(0.9,1.9,.1))
> res <- ImpShift(rbind(aa,bb,cc), NChun=2)
| | | 0% | |========== | 14% | |==================== | 29% | |============================== | 43% | |======================================== | 57% | |================================================== | 71% | |============================================================ | 86% | |======================================================================| 100%
>
>
>
>
>
> dev.off()
null device
1
>