R: Convert columns in a dataframe to class 'snp'

setupSNP {SNPassoc} | R Documentation

## Convert columns in a dataframe to class 'snp'

### Description

`setupSNP` Convert columns in a dataframe to class 'snp'

`summary.setupSNP` gives a summary for an object of class 'setupSNP' including allele names, major allele frequencie, an exact thest of Hardy-Weinberg equilibrium and percentage of missing genotypes

### Usage

    setupSNP(data, colSNPs, sort = FALSE, info, sep = "/", ...)

### Arguments

`data` | dataframe containing columns with the SNPs to be converted
`colSNPs` | Vector specifying which columns contain SNPs data
`sort` | should SNPs be sorted. Default is FALSE
`info` | if sort is TRUE a dataframe containing information about the SNPs regarding their genomic position and the gene where they are located
`sep` | character separator used to divide alleles in the genotypes
`...` | optional arguments

### Value

a dataframe of class 'setupSNP' containing converted SNP variables. All other variables will be unchanged.

### References

JR Gonzalez, L Armengol, X Sole, E Guino, JM Mercader, X Estivill, V Moreno. SNPassoc: an R package to perform whole genome association studies. Bioinformatics, 2007;23(5):654-5.

### See Also

`snp`

### Examples

     data(SNPs)
     myDat<-setupSNP(SNPs,6:40,sep="")

    #sorted SNPs and having genomic information
     data(SNPs.info.pos)
     myDat.o<-setupSNP(SNPs,6:40,sep="",sort=TRUE, info=SNPs.info.pos)

    # summary
     summary(myDat.o)

    # plot one SNP
      plot(myDat,which=2)

[Package SNPassoc version 1.9-2 Index]