Integrative container for expression plus genotype data. Genotypes
are stored in an efficient format defined in the snpStats package.
Objects from the Class
Objects can be created by calls of the form new("smlSet", assayData, phenoData, featureData, experimentData, annotation, protocolData, ...).
The make_smlSet function can also be used
to build smlSet instances.
Slots
smlEnv:
Object of class "environment" that has
a key smList element, to which a list of
SnpMatrix-class instances is bound.
annotation:
Object of class "character", describes
featureNames component in terms of the name of the
annotation package that can be used to decode expression probe names.
organism:
Object of class "character", a conventional
string.
assayData:
Object of class "AssayData",
manages the expression data. See AssayData-class.
phenoData:
Object of class "AnnotatedDataFrame" ,
manages sample level data. See AnnotatedDataFrame-class.
featureData:
Object of class "AnnotatedDataFrame",
manages metadata on expression probes.
experimentData:
Object of class "MIAxE", manages
metadata on experiment as a whole. See MIAxE-class.
protocolData:
Object of class "AnnotatedDataFrame",
additional storage for experimental protocol description.
See eSet-class.
.__classVersion__:
Object of class "Versions";
internal management of class version.
Extends
Class "eSet", directly.
Class "VersionedBiobase", by class "eSet", distance 2.
Class "Versioned", by class "eSet", distance 3.
Methods
[
signature(x = "smlSet", i = "ANY", j = "ANY", drop = "ANY"):
will restrict the content of the smlSet instance according to features
of the arguments supplied. If x is numeric or a probeId-class,
the expression content will be restricted. If y is numeric or
character, samples will be restricted accordingly.
combine
signature(x = "smlSet", y = "smlSet"): This method
attempts to amalgamate two smlSet instances in the appropriate way –
assuming that samples are disjoint.
nsFilter
signature(eset = "smlSet"): executes genefilter's
method (see nsFilter,ExpressionSet-method) on the
expression content, and then propagates the additional genotype and
sample level content unchanged.
smList
signature(x = "smlSet"): retrieves the list
of SnpMatrix instances defining the genotype content.
exprs
signature(x = "smlSet"): retrieves the matrix
of expression values
permEx
signature(sms = "smlSet"): uses sample()
to generate a permutation of sample indices so that expression data
are permuted against genotype data, but original unpermuted sample
identifiers are preserved; this is necessitated by the rematching
behavior of snp.rhs.tests
.
Author(s)
VJ Carey <stvjc@channing.harvard.edu>
Examples
showClass("smlSet")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGBase/smlSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: smlSet-class
> ### Title: Class '"smlSet"'
> ### Aliases: smlSet-class [,smlSet,ANY,ANY,ANY-method
> ### combine,smlSet,smlSet-method exprs,smlSet-method
> ### nsFilter,smlSet-method smList,smlSet-method smList
> ### permEx,smlSet-method permEx
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("smlSet")
Class "smlSet" [package "GGBase"]
Slots:
Name: smlEnv annotation organism
Class: environment character character
Name: assayData phenoData featureData
Class: AssayData AnnotatedDataFrame AnnotatedDataFrame
Name: experimentData protocolData .__classVersion__
Class: MIAxE AnnotatedDataFrame Versions
Extends:
Class "eSet", directly
Class "VersionedBiobase", by class "eSet", distance 2
Class "Versioned", by class "eSet", distance 3
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.