smlSet-class {GGBase}R Documentation

Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes

Description

Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes

Objects from the Class

Objects can be created by calls of the form new("smlSet", assayData, phenoData, featureData, experimentData, annotation, ...). These objects respond to interrogation on samples, expression values, SNP values, and other metadata.

Slots

smlEnv:
Object of class "environment" an environment with single key smList pointing to a list of package snpMatrix snp.matrix instances
snpLocPathMaker:
Object of class "function" obsolete
chromInds:
Object of class "numeric" numeric vector indicating what chromosomes are represented in the smlEnv
organism:
Object of class "character" informal, "Hs" recommended for human
snpLocPackage:
Object of class "character" tells what package houses the netCDF store for SNP location metadata
snpLocRef:
Object of class "character" tells the symbol exported by the snpLocPackage with which the external store connection can be retrieved. That symbol refers to a SQLite database connection.
activeSnpInds:
Object of class "numeric" redundant with chromInds slot
assayData:
Object of class "AssayData" intended to hold expression data coordinated with the smlEnv data
phenoData:
Object of class "AnnotatedDataFrame" standard sample-level data container from eSet design
featureData:
Object of class "AnnotatedDataFrame" standard feature-level metadata container, implied usage is for documenting the expresion data elements
experimentData:
Object of class "MIAME" standard metadata container from Biobase eSet design
annotation:
Object of class "character" vector of strings; element exprs gives the Bioconductor annotation package (.db type) for decoding expression feature identifiers.
.__classVersion__:
Object of class "Versions" class version tracking metadata

Extends

Class "eSet", directly. Class "VersionedBiobase", by class "eSet", distance 2. Class "Versioned", by class "eSet", distance 3.

Methods

smList
signature(x = "smlSet"): retrieves the actual list of snp.matrix entities
smlEnv
signature(x = "smlSet"): retrieves the environment holding snp.matrix entities

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

See Also

GGtools package makes extensive use of these classes and methods.

Examples

showClass("smlSet")

[Package GGBase version 2.0.4 Index]