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 organism
:"character"
informal,
"Hs" recommended for human 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
giving 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 signature(x = "smlSet")
: retrieves the
matrix of expression values signature(x = "smlSet", chr = "chrnum")
: retrieves the
raw matrix of genotype values (snp.matrix instance from
snpMatrix package combine
:getAlleles(smlSet, rsid)
:
We have included a [
method for snp.matrix instances
that accepts an rsid instance as a column selector.
VJ Carey <stvjc@channing.harvard.edu>
GGtools package makes extensive use of these classes and methods.
showClass("smlSet")