genoSet {SHARE}R Documentation

Genotype Sequence Set

Description

A class for storing genotype sequences and phenotype information.

Objects from the Class

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

Slots

genoSeq:
Object of class "data.frame" to store allelic data with sequence names as row names and SNP names as column names.
phenoData:
Object of class "data.frame" to store phenotype information for each genotype sequence. The names of the phenotype are used as the column names, and the row names should match the sequence names in the genoSeq slot.

Methods

genoSeq
signature(.Object = "genoSet"): extract the "data.frame" object in the genoSeq slot.
haplo
signature(.Object = "genoSet"): to estimate the haplotype sequences by EM algorithm in the haplo.stats package.
phenoData
signature(.Object = "genoSet"): return the "data.frame" object in the phenoData slot.

Author(s)

Ting-Yuan Liu

Examples

showClass("genoSet")
## See vignette for more details
## Not run: 
unphasedGeno <- new("genoSet",
                    genoSeq = data.frame(keremRandAllele),
                    phenoData = data.frame(CF=keremRandStatus)
                    )
unphasedGeno
## End(Not run)

[Package SHARE version 1.0.4 Index]