annotateCTSS {CAGEr} | R Documentation |
annotateCTSS
annotates the CTSS of a CAGEexp
object and
computes annotation statistics.
annotateConsensusClusters
annotates the consensus clusters
of a CAGEr object.
annotateCTSS(object, ranges) ## S4 method for signature 'CAGEexp,GRanges' annotateCTSS(object, ranges) annotateConsensusClusters(object, ranges) ## S4 method for signature 'CAGEexp,GRanges' annotateConsensusClusters(object, ranges)
object |
|
ranges |
A |
annotateCTSS
returns the input object with the following
modifications:
The Genomic Ranges of the tagCountMatrix
experiment gains an
annotation
metadata column, with levels such as promoter
,
exon
, intron
and unknown
. If the annotation has a gene_name
metadata, then a genes
column is also added, with gene symbols from
the annotation.
The sample metadata gets new columns, indicating total counts in each of
the annotation levels. If the annotation has a gene_name
metadata, then
a genes
column is added to indicate the number of different gene symbols
detected.
annotateConsensusClusters
returns the input object with the same
modifications as above.
Charles Plessy
CTSStoGenes
, and the exampleZv9_annot
example data.
Other CAGEr object modifiers:
CTSStoGenes()
,
CustomConsensusClusters()
,
aggregateTagClusters()
,
clusterCTSS()
,
cumulativeCTSSdistribution()
,
getCTSS()
,
normalizeTagCount()
,
quantilePositions()
,
summariseChrExpr()
Other CAGEr annotation functions:
plotAnnot()
,
ranges2annot()
,
ranges2genes()
,
ranges2names()
library(SummarizedExperiment) annotateCTSS(exampleCAGEexp, exampleZv9_annot) colData(exampleCAGEexp) annotateConsensusClusters(exampleCAGEexp, exampleZv9_annot) consensusClustersGR(exampleCAGEexp)