smlSet-class: Class '"smlSet"'

In GGBase: GGBase infrastructure for genetics of gene expression package GGtools

Description

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 <[e-mail]>

Examples

showClass("smlSet")

GGBase documentation built on Nov. 8, 2020, 5:45 p.m.