CorrelatedSNPs-class: Class '"CorrelatedSNPs"'

In FunciSNP: Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

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: [e-mail]); Houtan Noushmehr, PhD ([e-mail])

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")

FunciSNP documentation built on Nov. 8, 2020, 4:56 p.m.