TagSNP-class {FunciSNP} | R Documentation

## Class `"TagSNP"`

### Description

In the code snippets below, `x` is a `TagSNP` object. for the usage of `alt.allele`, `chr`, `position`, `ref.allele`, and `snpid` for the object `CorrelatedSNPs`, see `?CorrelatedSNPs-class`

### Usage

    ## S4 method for signature 'TagSNP'
    alt.allele(x)
    ## S4 replacement method for signature 'TagSNP'
    alt.allele(x) <- value
    ## S4 method for signature 'TagSNP'
    chr(x)
    ## S4 replacement method for signature 'TagSNP'
    chr(x) <- value
    ## S4 method for signature 'TagSNP'
    correlated.snps(x)
    ## S4 replacement method for signature 'TagSNP'
    correlated.snps(x) <- value
    ## S4 method for signature 'TagSNP'
    genotype(x)
    ## S4 replacement method for signature 'TagSNP'
    genotype(x) <- value
    ## S4 method for signature 'TagSNP'
    population(x)
    ## S4 replacement method for signature 'TagSNP'
    population(x) <- value
    ## S4 method for signature 'TagSNP'
    position(x)
    ## S4 replacement method for signature 'TagSNP'
    position(x) <- value
    ## S4 method for signature 'TagSNP'
    ref.allele(x)
    ## S4 replacement method for signature 'TagSNP'
    ref.allele(x) <- value
    ## S4 method for signature 'TagSNP'
    snpid(x)
    ## S4 replacement method for signature 'TagSNP'
    snpid(x) <- value
    ## S4 method for signature 'TagSNP'
    yafsnp.rsq(x)
    ## S4 replacement method for signature 'TagSNP'
    yafsnp.rsq(x) <- value
    ## S4 method for signature 'TagSNP'
    yafsnp.dprime(x)
    ## S4 replacement method for signature 'TagSNP'
    yafsnp.dprime(x) <- value
    ## S4 method for signature 'TagSNP'
    yafsnp.pvalue(x)
    ## S4 replacement method for signature 'TagSNP'
    yafsnp.pvalue(x) <- value
    ## S4 method for signature 'TagSNP'
    AFR.overlapping.snps.geno(x)
    ## S4 method for signature 'TagSNP'
    AMR.overlapping.snps.geno(x)
    ## S4 method for signature 'TagSNP'
    ASN.overlapping.snps.geno(x)
    ## S4 method for signature 'TagSNP'
    EUR.overlapping.snps.geno(x)

### Arguments

`x` | The TagSNP object from/on which to get/set snp information.
`value` | Examine the section "Slots" for the values taken by each method.

### Objects from the Class

Objects can be created by calls of the form `new("TagSNP", ...)`.

### Slots

`chromosome`:

  Object of class `"integer"` ~~

`position`:

  Object of class `"integer"` ~~

`snpid`:

  Object of class `"character"` ~~

`population`:

  Object of class `"character"` ~~

`ref.allele`:

  Object of class `"character"` ~~

`alt.allele`:

  Object of class `"character"` ~~

`genotype`:

  Object of class `"SnpMatrix"` ~~

`yafsnp.rsq`:

  Object of class `"dgCMatrix"` ~~

`yafsnp.dprime`:

  Object of class `"dgCMatrix"` ~~

`yafsnp.pvalue`:

  Object of class `"list"` ~~

`correlated.snps`:

  Object of class `"CorrelatedSNPs"` ~~

### Methods

alt.allele<-

  `signature(x = "TagSNP")`: ...

alt.allele

  `signature(x = "TagSNP")`: ...

chr<-

  `signature(x = "TagSNP")`: ...

chr

  `signature(x = "TagSNP")`: ...

correlated.snps<-

  `signature(x = "TagSNP")`: ...

correlated.snps

  `signature(x = "TagSNP")`: ...

genotype<-

  `signature(x = "TagSNP")`: ...

genotype

  `signature(x = "TagSNP")`: ...

population<-

  `signature(x = "TagSNP")`: ...

population

  `signature(x = "TagSNP")`: ...

position<-

  `signature(x = "TagSNP")`: ...

position

  `signature(x = "TagSNP")`: ...

ref.allele<-

  `signature(x = "TagSNP")`: ...

ref.allele

  `signature(x = "TagSNP")`: ...

R.squared.corrsnps<-

  `signature(x = "TagSNP")`: ...

R.squared.corrsnps

  `signature(x = "TagSNP")`: ...

show

  `signature(object = "TagSNP")`: ...

snpid<-

  `signature(x = "TagSNP")`: ...

snpid

  `signature(x = "TagSNP")`: ...

yafsnp.rsq<-

  `signature(x = "TagSNP")`: ...

yafsnp.rsq

  `signature(x = "TagSNP")`: ...

yafsnp.dprime<-

  `signature(x = "TagSNP")`: ...

yafsnp.dprime

  `signature(x = "TagSNP")`: ...

yafsnp.pvalue<-

  `signature(x = "TagSNP")`: ...

yafsnp.pvalue

  `signature(x = "TagSNP")`: ...

AFR.overlapping.snps.geno

  `signature(x = "TagSNP")`: ...

AMR.overlapping.snps.geno

  `signature(x = "TagSNP")`: ...

ASN.overlapping.snps.geno

  `signature(x = "TagSNP")`: ...

EUR.overlapping.snps.geno

  `signature(x = "TagSNP")`: ...

### Note

NA

### Author(s)

Simon G. Coetzee (maintainer: scoetzee@gmail.com); Houtan Noushmehr, PhD (houtan@usp.br)

### References

SG. Coetzee, SK. Rhie, BP. Berman, GA. Coetzee and H. Noushmehr, FunciSNP: An R/Bioconductor Tool Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs., Nucleic Acids Research, In press, 2012 (doi:10.1093/nar/gks542).

### See Also

`getFSNPs`, `FunciSNPplot`, `FunciSNPAnnotateSummary`, `FunciSNPtable`, `FunciSNPbed`

### Examples

    showClass("TagSNP")

[Package FunciSNP version 1.30.0 Index]