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Last data update: 2014.03.03

R: gets "scan" into a matrix

getInv-methods

R Documentation

gets "scan" into a matrix

Description

Each row of the matrix represents a trial segment of fixed window size, for which the inversion model has been fit. It lists the left and right brake-points and output of the fitting: Log-likelihood ratio, probability of inversion, entropy, BIC (Bayes Information Criterion) and number of haplotypes.

Usage

getInv(object, thBic, rnd, Like)

Arguments

`object`	`scan`. Cromosome scanned for inversions with trial segments of fixed window size.
`thBic`	`numeric`. BIC threshold above which data is retrieved.
`rnd`	`logic`. Whether round matrix elements.
`Like`	`numeric`. Log-likelihood ratio threshold above which data is retrieved.

Details

Matrix with output of scanInv. Each row corresponds to a trail segments with given brake points and significance measures for the inversion model.

Value

matrix.

Methods

signature(object = "scan"): returns matrix with output of inversion model for each trial segment

Examples

data(scanRes)
a<-getInv(scanRes,thBic=2500)
a

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/getInv-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getInv-methods
> ### Title: gets "scan" into a matrix
> ### Aliases: getInv-methods getInv,scan-method getInv
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(scanRes)
> a<-getInv(scanRes,thBic=2500)
> a
    LeftBP   RightBP   LogLike   Prob   Ent      BIC   NumHap
1    0.747     1.247  2712.429  0.586 2.608 2522.406       25
2    0.747     1.247  2712.429  0.586 2.608 2522.406       25
3    0.747     1.248  2712.429  0.586 2.608 2522.406       25
4    0.747     1.248  2712.429  0.586 2.463 2552.810       21
5    0.749     1.249  2712.429  0.586 2.502 2507.204       27
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>