Description Usage Arguments Objects from the Class Slots Methods Note Author(s) References See Also Examples

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`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 | ```
## 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)
``` |

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

.

`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"`

~~

- 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")`

: ...

NA

Simon G. Coetzee (maintainer: scoetzee@gmail.com); Houtan Noushmehr, PhD (houtan@usp.br)

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).

`getFSNPs`

, `FunciSNPplot`

, `FunciSNPAnnotateSummary`

, `FunciSNPtable`

, `FunciSNPbed`

1 | ```
showClass("TagSNP")
``` |

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