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]