GGBase (version 3.34.0)

make_smlSet: 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()

Value

Instance of smlSet-class.

Details

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

Examples

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