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Last data update: 2014.03.03

R: Inversion scan

scanInv

R Documentation

Inversion scan

Description

This function scans a whole chromosome in search for inversion events. The scan is done by fitting an inversion model to all segments in the chromosome with fixed length size.

Usage

scanInv(objectHaploCode, window, maxSteps = 30, geno = FALSE, saveRes = TRUE, saveBlocks=TRUE)

Arguments

`objectHaploCode`	Object of class `HaploCode` produced by the `codeHaplo` function.
`window`	`numeric`, size of the window in mega-basis.
`maxSteps`	`numeric`, maximum number of iteration in the EM algorithm for the inversion model
`geno`	`logical`. Whether the original data is genotypes or phases haplotypes.
`saveRes`	`logical`. Whether results should be saves into file `invRes.RData`
`saveBlocks`	`logical`. Whether save blocks for each candidate break point.

Details

The function processes the haplotypes coded in objectHaploCode. If subsequent re-runs are requires for different window sizes, this object can be omitted. The function will thus search the local directory for previous results to speed up further scans.

Value

object of class scan

Author(s)

Alejandro Caceres acaceres@creal.cat

Examples

data(hapCode)
window<-0.5
scanRes<-scanInv(hapCode,window=window,saveRes=FALSE,geno=FALSE,saveBlocks=FALSE)
scanRes
plot(scanRes)

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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> 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/scanInv.Rd_%03d_medium.png", width=480, height=480)
> ### Name: scanInv
> ### Title: Inversion scan
> ### Aliases: scanInv
> ### Keywords: constructor
> 
> ### ** Examples
> 
> data(hapCode)
> window<-0.5
> scanRes<-scanInv(hapCode,window=window,saveRes=FALSE,geno=FALSE,saveBlocks=FALSE)
-Scan for inversions-
-computing inversion model-

  Maximum brake-points to be tested 55
.
-computation done-
> scanRes
-Showing object of class: scan- 

Top 10 brake-points with highest Likelihood ratio:

            LeftBP         RightBP LogLike Prob BicDiff
1  0.75075-1.24021 1.25132-1.25160  527.85 0.78 345.412
2             <NA>            <NA>      NA   NA      NA
3             <NA>            <NA>      NA   NA      NA
4             <NA>            <NA>      NA   NA      NA
5             <NA>            <NA>      NA   NA      NA
6             <NA>            <NA>      NA   NA      NA
7             <NA>            <NA>      NA   NA      NA
8             <NA>            <NA>      NA   NA      NA
9             <NA>            <NA>      NA   NA      NA
10            <NA>            <NA>      NA   NA      NA

others:
window: length window ( 0.5 ) for searching inversion segments 
> plot(scanRes)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>