smlSet-class {GGtools} | R Documentation

## Class "smlSet" – efficient representation of SNP+expression data, based on Clayton snpMatrix package

### Description

Efficient representation of SNP+expression data, based on Clayton snpMatrix package. Supports efficient subsetting of whole-genome snp genotyping by chromosome.

### Objects from the Class

Objects can be created by calls of the form `new("smlSet", smlEnv, assayData, phenoData, featureData, experimentData, annotation, ...)`.

### Slots

`smlEnv`:
  Object of class `"environment"` – there is one key 'smList' with value a list of `snp.matrix` from snpMatrix package
`snpLocPathMaker`:
  OBSOLETE – IGNORE
`chromInds`:
  Object of class `"numeric"`, a numeric vector telling what chromosomes are represented. If chromosomes 20 and 21 are present, the values is c(20,21). X and Y are 23, 24.
`organism`:
  Object of class `"character"`; string such as Hs for modern humans.
`assayData`:
  Object of class `"AssayData"`; container for expression data as in ExpressionSet
`phenoData`:
  Object of class `"AnnotatedDataFrame"`; container for sample data as in ExpressionSet
`featureData`:
  Object of class `"AnnotatedDataFrame"`; container for expression feature data as in ExpressionSet
`experimentData`:
  Object of class `"MIAME"`; container for MIAME schema
`annotation`:
  Object of class `"character"`; vector with names `exprs` and `snps`; `exprs` should be the name of a SQLite-based Bioconductor annotation package
`.__classVersion__`:
  Object of class `"Versions"` ~~

### Extends

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

### Methods

[
  `signature(x = "smlSet")`: subsetting must be done with care. The usual idiom is `X[G, S]` where `G` restricts reporters and `S` restricts samples. Reporter restriction: At present one can use an instance of `chrnum` class to obtain a subsetted object with SNP data restricted to specified chromosomes. Sample restriction: works in the customary way for `eSet` instances.
exprs
  `signature(object = "smlSet")`: return the expression data matrix.
gwSnpScreen
  `signature(sym = "genesym", sms = "smlSet")`: Execute snpMatrix snp.rhs.tests for all SNP in the genome. Returns instance of gwSnpScreenResult.
cwSnpScreen
  `signature(sym = "genesym", sms = "smlSet", cnum="chrnum")`: Execute snpMatrix snp.rhs.tests for all SNP on the specific chromosome. Returns instance of cwSnpScreenResult.
nsamp
  `signature(x = "smlSet")`: returns number of samples.
rawSNP
  `signature(x = "smlSet", chrind = "numeric")`: returns byte (raw) representation of SNP data in snp.matrix format for specified chromosome.
getSnpLocs
  `signature(x = "smlSet")`: returns all relevant locations in order of rs numbers in the snp.matrices as a single vector
getSnpChroms
  `signature(x = "smlSet")`: returns all relevant chromosome assignments in order of rs numbers in the snp.matrices as a single vector
sampleNames
  `signature(object = "smlSet")`: returns vector of sample names.
show
  `signature(object = "smlSet")`: prints short report.
smList
  `signature(x = "smlSet")`: returns the list of snp.matrix encoding genotypes.
smlEnv
  `signature(x = "smlSet")`: returns the environment in which the smList list is contained.

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

### Examples

    #showClass("smlSet")
    data(hmceuB36.2021)
    rawSNP(hmceuB36.2021, 20)[1:5,1:5]
    exprs(hmceuB36.2021)[1:5,1:5]

[Package GGtools version 2.0.2 Index]