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Last data update: 2014.03.03

R: Overall classification

getClassif-methods

R Documentation

Overall classification

Description

Classifies into inverted or non-inverted populations each chromosome in the sample.

Usage

getClassif(object, thBic, wROI, bin,geno,id,nmod)

Arguments

`object`	`inversionList`. List of inversions obtained from a chromosome scan.
`thBic`	`numeric`. BIC threshold above which significant segments are chosen for the final classification
`wROI`	`numeric`. ROI number from the list to select classification
`bin`	`logic`. Whether binary or continous classification is retrieved
`geno`	`logic`. Whether inversion genotype is retrieved
`id`	`character`. Vector of subject IDs
`nmod`	`numeric`. number of trial segments to be used in the classification counting from the trial segments with highest BIC downwards.

Details

The overall classification of chromosomes into inverted and non-inverted populations is given by the weighted average of the classifications obtained for each trial segment in the ROI, with BIC greater than thBic.

Value

numeric. Vector with values between 0 and 1 representing membership to the non-inverted and inverted population respectively.

Methods

signature(object = "inversionList"): for each of the inversions of the list, it returns the classification of each chromosome.

Author(s)

Alejandro Caceres acaceres@creal.cat

Examples

data(invList)
r<-getClassif(invList)
head(r)

Results


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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/getClassif-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getClassif-methods
> ### Title: Overall classification
> ### Aliases: getClassif-methods getClassif,inversionList-method getClassif
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(invList)
> r<-getClassif(invList)

 getting mean classification across 18 models 

> head(r)
    id hom het homInv
1 sub1   0   1      0
2 sub2   0   1      0
3 sub3   0   1      0
4 sub4   0   1      0
5 sub5   1   0      0
6 sub6   0   1      0
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>