Class "GenoDatROI"

Description

GenoDat defined within an region of interest

Usage

ROIGenoDat(objectGenoDat, ROI)

Arguments

Details

ROIGenoDat is the constructor of the class.

Objects from the Class

object are created with calls to ROIGenoDat(objectGenoDat, ROI)

Slots

genoDat:

"matrix" . Genotypes

lociPos:

"numeric". Genomic coordinates

alleleSum:

"matrix". Total number of variant alleles in the population per SNP

noMissCount:

"matrix". Total number of subjects with no-missing values

ROI:

"numeric". Region of interest.

Extends

Class "GenoDat", directly.

Methods

initialize

signature(.Object = "GenoDatROI")

show

signature(object = "GenoDatROI")

Author(s)

Alejandro Caceres acaceres@creal.cat

See Also

GenoDat

Examples

data(gDat)
gDatROI<-ROIGenoDat(gDat,ROI=c(1268,1847))
gDatROI

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/GenoDatROI-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GenoDatROI-class
> ### Title: Class "GenoDatROI"
> ### Aliases: GenoDatROI-class initialize,GenoDatROI-method
> ###   show,GenoDatROI-method ROIGenoDat
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(gDat)
> gDatROI<-ROIGenoDat(gDat,ROI=c(1268,1847))
-Set up object of class: GenoDat- 
-Set up object class: GenoDatROI- 
> gDatROI
-Showing object of class: GenoDat- 

@genoDat: Genotype Data
   * integer matrix ~ 9 subjects by  4 probes
   * first elements = 
   [,1] [,2] [,3] [,4]
V1 1    0    1    0   
V2 1    1    1    0   
V3 2    0    2    0   
V4 1    1    1    0   
V5 1    1    1    0   
V6 0    0    0    0   
V7 0    0    0    1   
V8 2    0    2    0   
V9 0    0    1    0   

@lociPos: Probe Corrdinates
   * integer ~ 4 probes 
   * first 10 elements = 
  V3   V4   V5   V6 
1393 1467 1531 1761 

Other slots... 

@allaleSum: allele sum at each probe 
@noMissCount: number of no missings values 

-end showing GenoDat- 

-The object is defined in the ROI- 
 @ROI
[1] 1393 1761
-end showing ROIs- 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>