Simulated LRR and BAF data for 17,348 SNPs on chromosome 22.

Description

Simulated LRR and BAF data for 17,348 SNPs on chromosome 22. Two CNVs are simulated. One is from the 1001-th probe to the 1100-th probe, with copy number 1. The other one is from the 10,001-th probe to the 10,200-th probe, with copy number 3.

Usage

data(snpData)

Format

A data frame with 17,348 observations on the following 3 variables.

Name

a character vector of probe Names

LRR

a numeric vector of LRR values of each probe

BAF

a numeric vector of BAF of each probe

Examples

data(snpData)
data(snpInfo)

dim(snpData)
dim(snpInfo)

snpData[1:2,]
snpInfo[1:2,]

plotCN(pos=snpInfo$Position, LRR=snpData$LRR, BAF=snpData$BAF, 
main = "simulated data on Chr22")

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(genoCN)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genoCN/snpData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snpData
> ### Title: Simulated LRR and BAF data for 17,348 SNPs on chromosome 22.
> ### Aliases: snpData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(snpData)
> data(snpInfo)
> 
> dim(snpData)
[1] 17348     3
> dim(snpInfo)
[1] 17348     4
> 
> snpData[1:2,]
       Name        LRR         BAF
1 rs2334386 -0.2440655 1.000000000
2 rs9617528 -0.1422038 0.007824231
> snpInfo[1:2,]
             Name Chr Position   PFB
1075853 rs2334386  22 14430353 0.956
1075854 rs9617528  22 14441016 0.176
> 
> plotCN(pos=snpInfo$Position, LRR=snpData$LRR, BAF=snpData$BAF, 
+ main = "simulated data on Chr22")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>