FeatureSetExtensions-class: "FeatureSet" and "FeatureSet" Extensions

In jmacdon/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

Description

Classes to store data from Expression/Exon/SNP/Tiling arrays at the feature level.

Objects from the Class

The FeatureSet class is VIRTUAL. Therefore users are not able to create instances of such class.

Objects for FeatureSet-like classes can be created by calls of the form: new(CLASSNAME, assayData, manufacturer, platform, exprs, phenoData, featureData, experimentData, annotation, ...). But the preferred way is using parsers like read.celfiles and read.xysfiles.

Slots

manufacturer:

Object of class "character"

assayData:

Object of class "AssayData"

phenoData:

Object of class "AnnotatedDataFrame"

featureData:

Object of class "AnnotatedDataFrame"

experimentData:

Object of class "MIAME"

annotation:

Object of class "character"

.__classVersion__:

Object of class "Versions"

Methods

show

signature(.Object = "FeatureSet"): show object contents

bothStrands

signature(.Object = "SnpFeatureSet"): checks if object contains data for both strands simultaneously (50K/250K Affymetrix SNP chips - in this case it returns TRUE); if object contains data for one strand at a time (SNP 5.0 and SNP 6.0 - in this case it returns FALSE)

Author(s)

Benilton Carvalho

See Also

eSet, VersionedBiobase, Versioned

Examples

set.seed(1)
tmp <- 2^matrix(rnorm(100), ncol=4)
rownames(tmp) <- 1:25
colnames(tmp) <- paste("sample", 1:4, sep="")
efs <- new("ExpressionFeatureSet", exprs=tmp)

jmacdon/oligoClasses documentation built on Aug. 11, 2020, 12:32 a.m.