share-class {SHARE}R Documentation

SHARE output

Description

A class to store the result of SHARE algorithm

Objects from the Class

Objects can be created by calls of the form new("share", ...).

Slots

uhap:
Object of class "vector"; the concatenated haplotype sequences
weight:
Object of class "vector"; the weight of each haplotype
nFold:
Object of class "numeric"; the fold size specified while calling the cshare function to perform the cross-validation approach
maxSNP:
Object of class "numeric"; the maximum SNP size specified while calling the cshare functionused
deviance:
Object of class "vector"; the prediction deviance from cross-validation approach, or the BIC from BIC approach
bestsize:
Object of class "numeric"; the size of most informative SNPs
finalHap:
Object of class "data.frame"; the result of estimated haplotype sequences with the selected SNPs
finalHapFreq:
Object of class "vector"; the frequencies of the estimated haplotype sequences with the selected SNPs
finalHapTest:
Object of class "data.frame"; the hypothesis test results of the estimated haplotype sequences with the selected SNPs
globalP:
Object of class "numeric"; the global p-values
modelmethod:
Object of class "character"; the mothod of model selection specified while calling the cshare function
hap1
the code of first haplotype of each subject.
hap2
the code of first haplotype of each subject.
poolHapPair
Subject IDs.
nPosHapPair
vector for the count of haplotype pairs that map to each subject's marker genotypes.
post
vector of posterior probabilities of pairs of haplotypes for a person, given their marker phenotypes.
haploSeq:
Object of class "data.frame"; the original haplotype sequences with all SNPs
haploFreq:
Object of class "vector"; the frequencies of the original haplotype sequences with all SNPs
pheno:
Object of class "data.frame" to store the phenotype information
inherit:
Character string to show which mode of inheritance for haplotype effects is specified.

Extends

Class "haplo", directly. Class "haploSet", by class "haplo", distance 2.

Methods

dplot
signature(shareObj = "share"): to create the deviance plot to show the estimation of SNP size

Author(s)

James Y. Dai & Ting-Yuan Liu

See Also

cshare, haplo, haploSet

Examples

showClass("share")

## See vignette for more details
## Not run: 
dplot(unphasedKerem[["Cross-Val"]])
dplot(unphasedKerem[["BIC"]])
## End(Not run)

[Package SHARE version 1.0.4 Index]