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Last data update: 2014.03.03

R: construct an smlSet instance from existing resources

make_smlSet

R Documentation

construct an smlSet instance from existing resources

Description

construct an smlSet instance from existing resources, either using ExpressionSet and SnpMatrix instances, or a suitably structured package

Usage

make_smlSet(es, sml, organism = "Homo sapiens", harmonizeSamples = FALSE)

getSS(packname, chrs, renameChrs, probesToKeep=NULL, exFilter=function(x)x,
   wrapperEndo=NULL, checkValid=TRUE)

Arguments

`es`	instance of `ExpressionSet-class`
`sml`	named list of `SnpMatrix-class` instances
`organism`	conventional token for species
`harmonizeSamples`	logical indicating whether steps should be taken to be sure that the components represent identical sets of samples. can be time consuming so defaults to FALSE, in which case the user must be sure that the genotype and expression components are compatible in terms of sample content
`packname`	string naming the installed package from which expression and genotype data will be acquired
`chrs`	character vector naming the prefixes of genotype files to be used in the resulting smlSet instance; see notes below
`renameChrs`	character vector of same length as `chrs` specifying one-to-one renaming operation for genotype components in smlSet
`probesToKeep`	character vector identifying probes to be retained in the constructed smlSet – to be deprecated in favor of `exFilter`
`exFilter`	function that should accept and return `ExpressionSet`, will be executed just after `probesToKeep` filter if present
`wrapperEndo`	function that accepts and returns an smlSet instance, allowing any sort of transformation of contents acquired with `getSS`, executed after all assembly and filtering completed.
`checkValid`	logical, if TRUE, function will fail if created smlSet instance does not pass validObject()

Details

Packages that work with getSS can be created out of existing smlSet instances using externalize.

Value

Instance of smlSet-class.

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Examples

if ("GGtools" %in% installed.packages()[,1]) {
 s20 = getSS("GGtools", "20", renameChrs="chr20")
 s20
 make_smlSet( as(s20, "ExpressionSet"), smList(s20) )
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGBase/make_smlSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: make_smlSet
> ### Title: construct an smlSet instance from existing resources
> ### Aliases: make_smlSet getSS
> ### Keywords: models
> 
> ### ** Examples
> 
> if ("GGtools" %in% installed.packages()[,1]) {
+  s20 = getSS("GGtools", "20", renameChrs="chr20")
+  s20
+  make_smlSet( as(s20, "ExpressionSet"), smList(s20) )
+ }
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
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>