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Last data update: 2014.03.03

R: Codes haplotypes into decimal integers

codeHaplo

R Documentation

Codes haplotypes into decimal integers

Description

The function labels the haplotypes of size blockSize around each candidate brake-point. For labeling genotype data, the function takes objects of class genoDat as main argument. For phased data, this argument should be ignored and a file name passed instead.

Usage

codeHaplo(objectGenoDat, blockSize, minAllele, saveRes = TRUE, file = NULL, ROI,intSNP=FALSE,phasing="inversion&BP")

Arguments

`objectGenoDat`	`Genodat` object; if phased data then provide `file` instead
`blockSize`	`numeric`. number of SNPs flanking each side of each candidate brake-point. Default value 3
`minAllele`	`numeric`. minimum allele frequency for each probe to be considered as a candidate brake-point. Default value 0.1
`saveRes`	`logical`. Whether results should be saved in file `hapCode.RData`
`file`	`character`. File name with phased data
`ROI`	`numeric`. 2-vector specification passes a chromosome segment to be encoded. 4-vector specification passes the region of interest for the left brake-point (ROI[1] and ROI[2]) and the right brake-point (ROI[3] and ROI[4])
`intSNP`	`logical`. whether build flanking blocks of uniform SNP density across the genome.
`phasing`	`character`. Either c("ivenrsion&BP","forward", "forward&inverted"), defines the phasing strategy between all four flanking blocks of each break poin. ivenrsion&BP phases the internal flanking block first, then the external blocks to the internal bloks and match them. "forward" uses the blocks in the sequence assumming the forward population; in the inversion model, the backward population is obtained inverting the internal blocks. "forward&inverted" phases the forward and inverted population independently.

Details

When setUpGenodat is passed, the coding first computes the local haplotypes for each candidate-brake point form the genotype data and then encodes each haplotype into a decimal integer. The local haplotypes are computed with haplo.em form haplo.stats and assigns those with highest posterior probability to each chromosome. In the case of phased data, passed through file, no local haplotyping is needed and only the labeling is performed.

Value

Object of class HaploCode

Author(s)

Alejandro Caceres acaceres@creal.cat

References

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

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/codeHaplo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: codeHaplo
> ### Title: Codes haplotypes into decimal integers
> ### Aliases: codeHaplo
> ### Keywords: constructor
> 
> ### ** 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 
>