Class "GenoDat"

Description

Object that handles genotype data

Objects from the Class

Objects can be created by calls of the form setUpGenoDatFile or setUpGenoDatSNPmat .

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

Methods

plot

signature(x = "GenoDat"): Plots minor allele frequency

show

signature(object = "GenoDat"): shows data summary

Author(s)

Alejandro Caceres acaceres@creal.cat

See Also

setUpGenoDatFile, setUpGenoDatSNPmat

Examples

data(gDat)
gDat

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/GenoDat-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GenoDat-class
> ### Title: Class "GenoDat"
> ### Aliases: GenoDat-class plot,GenoDat-method show,GenoDat-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(gDat)
> gDat
-Showing object of class: GenoDat- 

@genoDat: Genotype Data
   * integer matrix ~ 9 subjects by  10 probes
   * first elements = 
   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
V1 0    1    1    0    1    0    1    1    0    0    
V2 1    0    1    1    1    0    0    1    0    0    
V3 0    0    2    0    2    0    0    2    0    0    
V4 1    0    1    1    1    0    0    1    0    0    
V5 0    0    1    1    1    0    0    1    0    0    
V6 0    0    0    0    0    0    0    0    0    0    
V7 1    0    0    0    0    1    0    0    1    1    
V8 0    0    2    0    2    0    0    2    0    0    
V9 0    0    0    0    1    0    0    1    0    0    

@lociPos: Probe Corrdinates
   * integer ~ 10 probes 
   * first 10 elements = 
  V1   V2   V3   V4   V5   V6   V7   V8   V9  V10 
 959 1268 1393 1467 1531 1761 1847 1987 2006 2030 

Other slots... 

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

-end showing GenoDat- 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>