R Graphical Manual

Browse All

Last data update: 2014.03.03

R: accBic computes "accuracy" from "inversionList"

accBic

R Documentation

accBic computes "accuracy" from "inversionList"

Description

accBic computes the accuracy of the classification of chromosomes into previously known inverted and non-inverted populations. The classification is obtained from a majority vote of the classifications produced by the trial segment models whose BIC is greater than a given threshold.

Usage

accBic(object, mem, classFile, nsub, npoints, geno, wROI)

Arguments

`object`	of class `inversionList`
`mem`	vector with the numbering of chromosomes known to have the inversion
`classFile`	an alternative to `mem`, it passes the file name containing the numbering of chromosomes known to have the inversion.
`nsub`	total number of subjects (= 2* total number of chromosomes)
`npoints`	number of BIC threshold between 0 and max (BIC) for which the accuracy is to be computed
`geno`	whether the accuracy is assessed for inversion genotype or inversion allele (phased data).
`wROI`	integer indicating the ROI number to be used. The total number of ROIs are the total number of components in the `object` list.

Value

accuracy

object of class accuracy

Author(s)

Alejandro Caceres acaceres@creal.cat

Examples

data(invList)
memFile <- system.file("extdata", "mem.txt", package = "inveRsion")
ac <- accBic(invList, classFile = memFile, nsub = 1000, npoints = 10)
plot(ac)

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(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/accBic.Rd_%03d_medium.png", width=480, height=480)
> ### Name: accBic
> ### Title: accBic computes "accuracy" from "inversionList"
> ### Aliases: accBic accBic-methods accBic,inversionList-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(invList)
> memFile <- system.file("extdata", "mem.txt", package = "inveRsion")
> ac <- accBic(invList, classFile = memFile, nsub = 1000, npoints = 10)

 computing accuracy for 10 bic thresholds: 
.........> plot(ac)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>