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

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")