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 'CAGEexp,GRanges'
annotateCTSS(object, ranges)

annotateConsensusClusters(object, ranges)

## S4 method for signature 'CAGEexp,GRanges'
annotateConsensusClusters(object, ranges)

Arguments

object

CAGEexp object.

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 1.99.0 Index]