CorrelatedSNPs-class {FunciSNP} | R Documentation

## Class `"CorrelatedSNPs"`

### Description

Class for CorrelatedSNPs

### Usage

    ## S4 method for signature 'CorrelatedSNPs'
    alt.allele(x)
    ## S4 replacement method for signature 'CorrelatedSNPs'
    alt.allele(x) <- value
    ## S4 method for signature 'CorrelatedSNPs'
    chr(x)
    ## S4 replacement method for signature 'CorrelatedSNPs'
    chr(x) <- value
    ## S4 method for signature 'CorrelatedSNPs'
    overlapping.features(x)
    ## S4 replacement method for signature 'CorrelatedSNPs'
    overlapping.features(x) <- value
    ## S4 method for signature 'CorrelatedSNPs'
    pop.genotype(x, population)
    ## S4 replacement method for signature 'CorrelatedSNPs'
    pop.genotype(x) <- value
    ## S4 method for signature 'CorrelatedSNPs'
    position(x)
    ## S4 replacement method for signature 'CorrelatedSNPs'
    position(x) <- value
    ## S4 method for signature 'CorrelatedSNPs'
    ref.allele(x)
    ## S4 replacement method for signature 'CorrelatedSNPs'
    ref.allele(x) <- value
    ## S4 method for signature 'CorrelatedSNPs'
    snpid(x)
    ## S4 replacement method for signature 'CorrelatedSNPs'
    snpid(x) <- value

### Arguments

`x` | The CorrelatedSNPs object from/on which to get/set snp information.
`value` | Examine the section "Slots" for the values taken by each method.
`population` | Population for which to set/get genotype information, either "AFR", "AMR", "ASN", "EUR" or "ALL".

### Objects from the Class

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

### Slots

`chromosome`:

  Object of class `"integer"` ~~

`position`:

  Object of class `"integer"` ~~

`snpid`:

  Object of class `"character"` ~~

`ref.allele`:

  Object of class `"character"` ~~

`alt.allele`:

  Object of class `"character"` ~~

`overlapping.features`:

  Object of class `"GRanges"` ~~

`genotype`:

  Object of class `"CorrGeno"` ~~

### Methods

alt.allele<-

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

alt.allele

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

chr<-

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

chr

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

overlapping.features<-

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

overlapping.features

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

pop.genotype<-

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

pop.genotype

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

position<-

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

position

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

ref.allele<-

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

ref.allele

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

snpid<-

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

snpid

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

### 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("CorrelatedSNPs")

[Package FunciSNP version 1.28.0 Index]