Search for the optimal sample order for different gene clusters

Description

Search for the optimal sample order for different gene clusters

Usage

OscopeENI(KMRes, Data, ClusterUse=NULL, Ndg=3, NChun=4, RdmStart=FALSE,
N=20000, NCThre=1000, parallel=FALSE, parallelParam=NULL)

Arguments

Value

This function performs the extended nearest insertion (ENI) and 2-opt algorithm to all clusters (or a subset of picked clusters) identified by OscopeKM function. The function will recover independent orders to each of the clusters. For each cluster, the ENI algorithm will be applied to search for the optimal sample order which minimizes the MSE of sliding polynomial regression (SPR). This function will call PipeShiftCDF() function, which fits SPR to expression of each gene/isoform within a cluster. 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 of PipeShiftCDF() returns the optimal order which provides the smallest SPR MSE. The 2-opt algorithm will then be applied to improve the optimal order searching of the ENI. In each iteration, the 2-opt algorithm will randomly choose two points (samples), the flip the samples between these two points. The new order will be adapted if it provides smaller SPR MSE. The output returns the optimal order for each cluster of interest. It is a list with multiple sublists, in which each sublist includes the recovered order of the corresponding cluster in ClusterUse. If ClusterUse is not specified, the k th sublist shows the recovered order in KMRes

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))
dd <- sin(seq(1.2,2.2,.1))
res <- OscopeENI(list(c1=c("aa","bb"),c2=c("cc","dd")), rbind(aa,bb,cc,dd), NChun=2, N=50)

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.

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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/OscopeENI.Rd_%03d_medium.png", width=480, height=480)
> ### Name: OscopeENI
> ### Title: Search for the optimal sample order for different gene clusters
> ### Aliases: OscopeENI
> 
> ### ** Examples
> 
> aa <- sin(seq(0,1,.1))
> bb <- sin(seq(0.5,1.5,.1))
> cc <- sin(seq(0.9,1.9,.1))
> dd <- sin(seq(1.2,2.2,.1))
> res <- OscopeENI(list(c1=c("aa","bb"),c2=c("cc","dd")), rbind(aa,bb,cc,dd), NChun=2, N=50)
ENI of c1; inserting samples:
   |                                                                               |                                                                      |   0%   |                                                                               |==========                                                            |  14%   |                                                                               |====================                                                  |  29%   |                                                                               |==============================                                        |  43%   |                                                                               |========================================                              |  57%   |                                                                               |==================================================                    |  71%   |                                                                               |============================================================          |  86%   |                                                                               |======================================================================| 100%
2-opt of c1
updated at iteration 2 ; ENI of c2; inserting samples:
   |                                                                               |                                                                      |   0%   |                                                                               |==========                                                            |  14%   |                                                                               |====================                                                  |  29%   |                                                                               |==============================                                        |  43%   |                                                                               |========================================                              |  57%   |                                                                               |==================================================                    |  71%   |                                                                               |============================================================          |  86%   |                                                                               |======================================================================| 100%
2-opt of c2
updated at iteration 1 ; updated at iteration 16 ; updated at iteration 40 ; > 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>