Class "HaploCode"

Description

The object stores the haplotype coding for each of the candidate brake-points. It is typically generated by calling the function codeHaplo on a GenoDat object.

Objects from the Class

Objects can be created by calls of codeHaplo(objectGenoDat, blockSize, minAllele, saveRes = TRUE, file = NULL, ROI)

Slots

haploCode:

Object of class "matrix" Haplotype coding into decimal integers

blockSize:

Object of class "numeric" block size of SNP used to identify the haplotype of each candidate brake-point.

minAllele:

Object of class "numeric" minimum allele above which candidate brake-points are considered

Methods

initialize

signature(.Object = "HaploCode"): Internal, users should use codeHaplo

show

signature(object = "HaploCode"): shows HaploCode

Author(s)

Alejandro Caceres acaceres@creal.cat

See Also

codeHaplo, GenoDat

Examples

data(gDat)
hapCode <-codeHaplo(gDat,blockSize=3,minAllele=0.3,saveRes=FALSE)
hapCode

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/HaploCode-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: HaploCode-class
> ### Title: Class "HaploCode"
> ### Aliases: HaploCode-class initialize,HaploCode-method
> ###   show,HaploCode-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(gDat)
> hapCode <-codeHaplo(gDat,blockSize=3,minAllele=0.3,saveRes=FALSE)
-Code haplotypes-
  preparing data
  Number of brakepoints: 3
...
-computation done-
> hapCode
-Showing object of class: HaploCode- 

@haploCode: Binary code for haplotypes of brake-points flanked by SNP blocks
   * numeric matrix ~ 18 chromosomes by  3 brake points
   * first elements = 
      0.001393 0.001467 0.001467 0.001531 0.001531 0.001761
 [1,] 1        0        0        1        0        1       
 [2,] 2        2        6        4        5        2       
 [3,] 1        2        0        0        0        0       
 [4,] 4        4        3        4        7        1       
 [5,] 1        2        2        4        5        1       
 [6,] 1        2        2        4        5        1       
 [7,] 1        2        0        0        0        0       
 [8,] 4        4        3        4        7        1       
 [9,] 0        2        0        0        0        0       
[10,] 1        4        3        4        7        1       
[11,] 0        0        0        0        0        0       
[12,] 0        0        0        0        0        0       
[13,] 0        0        0        0        0        0       
[14,] 4        1        0        2        0        4       
[15,] 1        2        2        4        5        1       
[16,] 1        2        2        4        5        1       
[17,] 0        0        0        0        0        0       
[18,] 0        2        0        4        1        1       
attr(,"locilim")
     [,1] [,2]
[1,]    1    6
[2,]    2    7
[3,]    3    8
attr(,"phasing")
[1] inversion&BP

@blockSize: Block Size of  3 SNPs 
@minAllele: Brake points with minimum allele frequency of  0.3 
 
-end showing HaploCode- 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>