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
organism:
Object of class "character" informal, "Hs" recommended for human
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 giving 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
exprs
signature(x = "smlSet"): retrieves the matrix of expression values
snps
signature(x = "smlSet", chr = "chrnum"): retrieves the raw matrix of genotype values (snp.matrix instance from snpMatrix package
combine:
concatenates expression data and forms intersection of SNP sets
getAlleles(smlSet, rsid):
returns A/B notations for SNP determined by rsid

Note

We have included a [ method for snp.matrix instances that accepts an rsid instance as a column selector.

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 3.4.0 Index]