annotateCTSS {CAGEr}R Documentation

Annotate and compute summary statistics

Description

annotateCTSS annotates the CTSS of a CAGEexp object and computes annotation statistics.

annotateConsensusClusters annotates the consensus clusters of a CAGEr object.

Usage

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)

Arguments

object

CAGEexp object (CAGEsets are not supported).

ranges

A GRanges object, optionally containing gene_name, type and transcript_type metadata.

Value

annotateCTSS returns the input object with the following modifications:

annotateConsensusClusters returns the input object with the same modifications as above.

Author(s)

Charles Plessy

See Also

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

Examples

library(SummarizedExperiment)
annotateCTSS(exampleCAGEexp, exampleZv9_annot)
colData(exampleCAGEexp)

annotateConsensusClusters(exampleCAGEexp, exampleZv9_annot)
consensusClustersGR(exampleCAGEexp)


[Package CAGEr version 1.30.3 Index]