TagSNP-class: Class '"TagSNP"'

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

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: [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("TagSNP")

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