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
`chromInds`:
  Object of class `"numeric"` numeric vector indicating what chromosomes are represented in the `smlEnv`
`snpNames`:
  Object of class `"character"` list of character strings naming SNPs genotyped in smList element of smlEnv
`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
`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 3.0.0 Index]