R: Class '"CorrelatedSNPs"'

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

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).

Examples

showClass("CorrelatedSNPs")

[Package FunciSNP version 1.32.0 Index]

Class "CorrelatedSNPs"