annotateCTSS {CAGEr} | R Documentation |
annotateCTSS
annotates the CTSS of a CAGEr object and computes
annotation statistics.
annotateConsensusClusters
annotates the consensus clusters
of a CAGEr object.
annotateCTSS(object, ranges) ## S4 method for signature 'CAGEset,ANY' annotateCTSS(object, ranges) ## S4 method for signature 'CAGEexp,GRanges' annotateCTSS(object, ranges) annotateConsensusClusters(object, ranges) ## S4 method for signature 'CAGEset,ANY' 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 a
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 data get 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
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)