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 ~

### See Also

### Examples

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

[Package GeneticsBase version 1.0.0 Index]