smlSet-class {GGBase} | R Documentation |
Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes
Objects can be created by calls of the form new("smlSet", assayData, phenoData, featureData, experimentData, annotation, ...)
.
These objects respond to interrogation on samples, expression values,
SNP values, and other metadata.
smlEnv
:"environment"
an environment
with single key smList
pointing to a list of
package snpMatrix snp.matrix instances snpLocPathMaker
:"function"
obsolete chromInds
:"numeric"
numeric
vector indicating what chromosomes are represented in the smlEnv
organism
:"character"
informal,
"Hs" recommended for human snpLocPackage
:"character"
tells
what package houses the netCDF store for SNP location metadata snpLocRef
:"character"
tells
the symbol exported by the snpLocPackage with which the external store connection
can be retrieved. That symbol refers to a SQLite database connection.activeSnpInds
:"numeric"
redundant with
chromInds slot assayData
:"AssayData"
intended
to hold expression data coordinated with the smlEnv data phenoData
:"AnnotatedDataFrame"
standard sample-level data container from eSet design featureData
:"AnnotatedDataFrame"
standard feature-level metadata container, implied usage is for documenting
the expresion data elements experimentData
:"MIAME"
standard
metadata container from Biobase eSet design annotation
:"character"
vector
of strings; element exprs gives the Bioconductor annotation package
(.db type) for decoding expression feature identifiers. .__classVersion__
:"Versions"
class
version tracking metadata
Class "eSet"
, directly.
Class "VersionedBiobase"
, by class "eSet", distance 2.
Class "Versioned"
, by class "eSet", distance 3.
signature(x = "smlSet")
: retrieves the
actual list of snp.matrix entities signature(x = "smlSet")
: retrieves the
environment holding snp.matrix entities VJ Carey <stvjc@channing.harvard.edu>
GGtools package makes extensive use of these classes and methods.
showClass("smlSet")