TagSNP-class {FunciSNP} | R Documentation |
"TagSNP"
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
## 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"
~~
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(object = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
signature(x = "TagSNP")
: ...
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
showClass("TagSNP")