Class "scan"

Description

Results from scanning the genome with the inversion model for trial segments of fixed window size.

Objects from the Class

scan objects are typically generated by callings to the constructor function scanInv

Slots

leftBP:

Object of class "matrix" Left brake-point coordinates (right SNP)

rightBP:

Object of class "matrix" Right brake-point coordinates (right SNP)

leftBP2:

Object of class "matrix" Left brake-point coordinates (left SNP)

rightBP2:

Object of class "matrix" Right brake-point coordinates (right SNP)

LogLike:

Object of class "matrix" Log-likelihood ratio for each trial segment

prob:

Object of class "matrix" probability of no-inversion for each trial segment

ent:

Object of class "matrix" entropy for each trial segment

entTh:

Object of class "matrix" entropy threshold for each trial segment

bic:

Object of class "matrix" BIC for each trial segment

window:

Object of class "numeric" window size

Methods

getInv

signature(object = "scan"): gets scan results into a matrix

getROIs

signature(object = "scan"): get regions of interest, overlapping trial segments with significant BIC

listInv

signature(object = "scan"): determines the inversion sequence for each ROI

plot

signature(x = "scan"): plots scan results, set option which=c("bic","log","prob","ent") to plot BIC, log-likelihood ratio, probability of no inversion or entropy; and thBic=0 to plot segments with BIC greater than 0

show

signature(object = "scan"): shows scan results for each ROI

Author(s)

Alejandro Caceres acaceres@creal.cat

See Also

listInv, HaploCode, getInv, getROIs

Examples

data(scanRes)
scanRes
plot(scanRes,which="bic",thBic=0)

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)

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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
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> library(inveRsion)
Loading required package: haplo.stats


Hola!

welcome to inevRsion package. 
 
 

type: manual() for full manual 
      vignette("inveRsion") for a quick start 

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/inveRsion/scan-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: scan-class
> ### Title: Class "scan"
> ### Aliases: scan-class plot,scan-method show,scan-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(scanRes)
> scanRes
-Showing object of class: scan- 

Top 10 brake-points with highest Likelihood ratio:

            LeftBP         RightBP LogLike  Prob  BicDiff
1  0.75075-0.75124 1.25132-1.25160 2714.85 0.577 2464.021
2  0.74661-0.74661 1.24666-1.24687 2712.43 0.586 2522.406
3  0.74661-0.74690 1.24666-1.24687 2712.43 0.586 2522.406
4  0.74690-0.74721 1.24760-1.24881 2712.43 0.586 2522.406
5  0.74721-0.74776 1.24760-1.24881 2712.43 0.586 2552.810
6  0.74852-0.74890 1.24886-1.24911 2712.43 0.586 2507.204
7  0.74890-0.74891 1.24911-1.24930 2712.43 0.586 2476.800
8  0.74944-0.75066 1.24951-1.24951 2712.43 0.586 2431.195
9  0.75772-0.75789 1.25803-1.25821 2712.43 0.586 2438.796
10 0.74891-0.74944 1.24911-1.24930 2708.76 0.581 2473.131

others:
window: length window ( 0.5 ) for searching inversion segments 
> plot(scanRes,which="bic",thBic=0)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>