Annotate and compute summary statistics

Description

annotateCTSS annotates the CTSS of a CAGEr 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

Value

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.

Author(s)

Charles Plessy

See Also

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)