Primary class structure, and associated methods
is used to denote “SNP matrix list” integrative
container for expression plus genotype data. The
class is defined in Clayton’s package.
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## Class "smlSet" [package "GGBase"]
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## Slots:
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## Name: smlEnv annotation organism
## Class: environment character character
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## Name: assayData phenoData featureData
## Class: AssayData AnnotatedDataFrame AnnotatedDataFrame
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## Name: experimentData protocolData .__classVersion__
## Class: MIAxE AnnotatedDataFrame Versions
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## Extends:
## Class "eSet", directly
## Class "VersionedBiobase", by class "eSet", distance 2
## Class "Versioned", by class "eSet", distance 3
## Function: [ (package base)
## x="smlSet", i="ANY", j="ANY", drop="ANY"
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## Function: clipPCs (package GGBase)
## x="smlSet", inds2drop="numeric", center="logical"
## x="smlSet", inds2drop="numeric", center="missing"
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## Function: combine (package BiocGenerics)
## x="smlSet", y="smlSet"
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## Function: exprs (package Biobase)
## object="smlSet"
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## Function: nsFilter (package genefilter)
## eset="smlSet"
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## Function: permEx (package GGBase)
## sms="smlSet"
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## Function: plot_EvG (package GGBase)
## gsym="genesym", rsid="rsid", sms="smlSet"
## gsym="probeId", rsid="rsid", sms="smlSet"
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## Function: smList (package GGBase)
## x="smlSet"
Genotype data are stored in a list in the environment
to diminish copying as functions are called on the instance.
Example data structure
Expression data were published by the Wellcome Trust GENEVAR project
in 2007. Genotype data are from HapMap phase II.
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## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB
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## which
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## Filter, Find, Map, Position, Reduce, anyDuplicated, append,
## as.data.frame, basename, cbind, colnames, dirname, do.call,
## duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
## lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
## pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
## tapply, union, unique, unsplit, which, which.max, which.min
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## getCall
## SnpMatrix-based genotype set:
## number of samples: 90
## number of chromosomes present: 1
## annotation: illuminaHumanv1.db
## Expression data dims: 47293 x 90
## Total number of SNP: 119921
## Phenodata: An object of class 'AnnotatedDataFrame'
## sampleNames: NA06985 NA06991 ... NA12892 (90 total)
## varLabels: famid persid ... male (7 total)
## varMetadata: labelDescription