summariseChrExpr: Expression levels by chromosomes

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

Counts the number of molecules detected per chromosome, normalises by library size and stores the raw and normalised results in the CAGEr object.

Usage

summariseChrExpr(object)

## S4 method for signature 'CAGEexp'
summariseChrExpr(object)

Arguments

object

A CAGEexp object (CAGEset objects are not supported).

Value

Modifies the CAGEexp by adding a “seqNameTotals” experiment containing matrices where rows represent chromosomes and columns represent samples.

Author(s)

Charles Plessy

See Also

seqNameTotals

Other CAGEr object modifiers: CTSStoGenes, CustomConsensusClusters, aggregateTagClusters, annotateCTSS, clusterCTSS, cumulativeCTSSdistribution, getCTSS, normalizeTagCount, quantilePositions

Examples

summariseChrExpr(exampleCAGEexp)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.