annotationByGenicParts-class: An S4 class for overlap of target features with gene...
In vd4mmind/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results
Description
Slots
See Also
Examples
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
membersa matrix showing overlap
of target features with gene annotation features
annotationa named vector of percentages of
overlap between feature and gene annotation
precedencea named vector of percentages of
overlap between feature and gene annotation
num.annotationa named vector of numbers of
overlap between feature and gene annotation
num.precedencea named vector of numbers of
overlap between feature and gene annotation
no.of.OlapFeata named vector of numbers of
overlap between gene annotation and the feature
perc.of.OlapFeata named vector of
percentages of overlap between gene annotation and the
feature
dist.to.TSSa 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
1
2
3
4
5
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)
vd4mmind/methylkit documentation built on May 3, 2019, 4:57 p.m.
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Description Slots See Also Examples
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
membersa matrix showing overlap of target features with gene annotation features
annotationa named vector of percentages of overlap between feature and gene annotation
precedencea named vector of percentages of overlap between feature and gene annotation
num.annotationa named vector of numbers of overlap between feature and gene annotation
num.precedencea named vector of numbers of overlap between feature and gene annotation
no.of.OlapFeata named vector of numbers of overlap between gene annotation and the feature
perc.of.OlapFeata named vector of percentages of overlap between gene annotation and the feature
dist.to.TSSa 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
1 2 3 4 5 | 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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