methylKit (version 0.9.5)

annotationByGenicParts-class: An S4 class for overlap of target features with gene annotation

Description

This object is desgined to hold basic statistics and information about genomic feature overlaps. It extends annotationByFeature class. The class contains an additional slot for data containing distance to nearest transcription start site (TSS).

Slots

members

a matrix showing overlap of target features with gene annotation features

annotation

a named vector of percentages of overlap between feature and gene annotation

precedence

a named vector of percentages of overlap between feature and gene annotation

num.annotation

a named vector of numbers of overlap between feature and gene annotation

num.precedence

a named vector of numbers of overlap between feature and gene annotation

no.of.OlapFeat

a named vector of numbers of overlap between gene annotation and the feature

perc.of.OlapFeat

a named vector of percentages of overlap between gene annotation and the feature

dist.to.TSS

a data frame showing distances to TSS and gene/TSS names and strand

See Also

see annotate.WithGenicParts on how to create this object, see following functions that operates on this object getTargetAnnotationStats, getMembers, getAssociationWithTSS, getTargetAnnotationStats, codegetFeatsWithTargetsStats,plotTargetAnnotation

Examples

# NOT RUN {
data(methylKit)
gene.obj=read.transcript.features(system.file("extdata", "refseq.hg18.bed.txt", package = "methylKit"))

# the following function returns an annotationByGenicParts object
ann=annotate.WithGenicParts(methylDiff.obj, gene.obj)
# }