smlSet-class {GGBase} | R Documentation

## Class `"smlSet"`

### 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 <stvjc@channing.harvard.edu>

### Examples

    showClass("smlSet")

[Package GGBase version 3.52.0 Index]