A dummy snp dataset that provides an example of the input snp data used by the package

Description

A dummy dataset of three SNPs, as a matrix of 3 column and 150 rows. The genotypes are in 0/1/2 format (0 for “AA”, 1 for “Aa” and 2 for “aa”, where A and a correspond, arbitrarily, to the two alleles). The data has been randomly generated, for instructional purposes only, and do not yield a significant association with any of the example phenotypes.

Usage

data(snps)

Format

A data frame with 150 genotype observations.

rsID1

a numeric vector

rsID2

a numeric vector

rsID3

a numeric vector

Details

The 150 genotypes in 'snp' correspond to the phenotype data on 150 individuals in ‘pheno’, i.e. one individual for each line. Please note the following important points: genotype data must be in matrix format, with one row for each individual and as many columns for each SNP. In the case of one single genotype the data must still conform to this format, as a matrix of as many rows as individuals and one single column for the one genotype present. A second important point is that the column names must be the rsID of the SNP for genotypes in the 0/1/2 format. Further options of genotype format (incorporating raw genotype data, and CNV genotypes) will be available and documented in future releases.

Examples

data(snps)
dim(snps)
colnames(snps)

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(MultiPhen)
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 4.4-1).
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MultiPhen/snps.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snps
> ### Title: A dummy snp dataset that provides an example of the input snp
> ###   data used by the package
> ### Aliases: snps
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(snps)
> dim(snps)
[1] 150   3
> colnames(snps)
[1] "1_1" "1_2" "1_3"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>