geneSet-class {GeneticsBase}R Documentation

Class "geneSet", a class for genetics data

Description

A fundamental data structure for genetic data

Objects from the Class

Objects can be created by calls of the form new("geneSet", ...). ~~ describe objects here ~~

Slots

callCodes:
matrix of positive integers, giving genotype calls. Each row is a locus (marker); each column is an individual (sample). Each element is a row index into a matrix in the list of translation tables stored in the transTables slot. Must have row and column names.
errorMetrics:
numeric matrix, parallel to the callCodes matrix. Each element gives an uncertainty measure for the corresponding element of the callCodes matrix. Must have row and column names.
transTables:
list of code translation tables. The list must have names. Each component is a matrix, and must include a column named "levels".
missingCodes:
list of allele missing-value codes, parallel to the transTables list. The list must have the same names as the list in the transTables slot. Each component is a character vector. Any allele symbol in component "abc" of the transTables list that appears in component "abc" of the missingCodes list is to be interpreted as a missing value by functions operating on the geneSet object. An empty list will be interpreted to mean that the data contains no missing values.
sampleInfo:
Object of class "data.frame"
markerInfo:
a dataframe, with one row for each row in the callCodes matrix. Must include columns "Name" and "TransTable".
studyInfo:
Object of class "list" ~~
description:
Object of class "character" ~~
notes:
Object of class "character" ~~
ploidy:
Object of class "numeric" ~~
phase:
1. Yes/No for all (logical scalar) 2. Yes/No for each Marker (logical vector) 3. phaseObject (TBD): observation by marker by phase probabilities + definitions of contigs + probability of contigs

Methods

HWE
signature(object = "geneSet"): Hardy-Weinberg Equilibrium Significance Test
LD
signature(object = "geneSet"): ...
LDband
signature(object = "geneSet"): ...
LDdist
signature(object = "geneSet"): ...
[
signature(x = "geneSet"): ...
[[
signature(x = "geneSet"): ...
alleleCount
signature(object = "geneSet"): ...
alleleLevels
signature(object = "geneSet"): ...
alleles
signature(object = "geneSet"): ...
callCodes
signature(object = "geneSet"): ...
callCodes<-
signature(object = "geneSet"): ...
carrier
signature(object = "geneSet"): ...
description
signature(object = "geneSet"): ...
description<-
signature(object = "geneSet"): ...
dominant
signature(object = "geneSet"): ...
errorMetrics
signature(object = "geneSet"): ...
errorMetrics<-
signature(object = "geneSet"): ...
genotypeLevels
signature(object = "geneSet"): ...
genotypes
signature(object = "geneSet"): ...
head
signature(x = "geneSet"): ...
heterozygote
signature(object = "geneSet"): ...
homozygote
signature(object = "geneSet"): ...
markerInfo
signature(object = "geneSet"): ...
markerInfo<-
signature(object = "geneSet"): ...
markerNames
signature(object = "geneSet"): ...
missingCodes
signature(object = "geneSet"): ...
missingCodes<-
signature(object = "geneSet"): ...
nallele
signature(object = "geneSet"): ...
nmarker
signature(object = "geneSet"): ...
nobs
signature(x = "geneSet"): ...
notes
signature(object = "geneSet"): ...
notes<-
signature(object = "geneSet"): ...
phase
signature(object = "geneSet"): ...
phase<-
signature(object = "geneSet"): ...
ploidy
signature(object = "geneSet"): ...
ploidy<-
signature(object = "geneSet"): ...
recessive
signature(object = "geneSet"): ...
sampleInfo
signature(object = "geneSet"): ...
sampleInfo<-
signature(object = "geneSet"): ...
show
signature(object = "geneSet"): ...
studyInfo
signature(object = "geneSet"): ...
studyInfo<-
signature(object = "geneSet"): ...
tail
signature(x = "geneSet"): ...
transTables
signature(object = "geneSet"): ...
transTables<-
signature(object = "geneSet"): ...

Note

~~further notes~~

Author(s)

J.Cheng, modified by S. Chasalow, and Gregory R. Warnes <warnes@bst.rochester.edu>

References

~put references to the literature/web site here ~

Examples

##---- Should be DIRECTLY executable !! ----

[Package GeneticsBase version 1.6.0 Index]