methylKit (version 0.99.2)

annotationByFeature-class: An S4 class for overlap of target features with a generic annotation

Description

This object is desgined to hold statistics and information about genomic feature overlaps it extends list class.

Slots

members

a matrix showing overlap of target features with annotation genomic features

annotation

a named vector of percentages of overlap between feature and annotation

'

precedence

a named vector of percentages of overlap between feature and annotation

num.annotation

a named vector of numbers of overlap between feature and annotation

num.precedence

a named vector of numbers of overlap between feature and annotation

no.of.OlapFeat

vector

perc.of.OlapFeat

vector

See Also

see annotateWithFeatureFlank and annotateWithFeature on how to create this object. see following functions that operates on this object: getMembers, getTargetAnnotationStats, getFeatsWithTargetsStats, plotTargetAnnotation

Examples

# NOT RUN {
data(methylKit)
cpg.obj=readFeatureFlank(system.file("extdata", "cpgi.hg18.bed.txt", 
                            package = "methylKit"),
                            feature.flank.name=c("CpGi","shores"))

# the following function returns annotationByFeature object
ann=annotateWithFeatureFlank(methylDiff.obj,cpg.obj$CpGi,cpg.obj$shores,
                               feature.name="CpGi",flank.name="Shores")
ann

# }