TSSlogo: TSS logo

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

TSS logo

Description

Plot the sequence logo of the region flanking the TSS. When this function is given tag clusters or consensus clusters, it uses the dominant peak as the transcription start site.

Usage

TSSlogo(x, upstream = 10, downstream = 10)

## S4 method for signature 'CAGEexp'
TSSlogo(x, upstream = 10, downstream = 10)

## S4 method for signature 'TagClusters'
TSSlogo(x, upstream = 10, downstream = 10)

## S4 method for signature 'ConsensusClusters'
TSSlogo(x, upstream = 10, downstream = 10)

## S4 method for signature 'CTSS'
TSSlogo(x, upstream = 10, downstream = 10)

Arguments

x	A CTSS, a TagClusters or a ConsensusClusters object.
upstream	Number of bases to plot upstream the TSS.
downstream	Number of bases to plot downstream the TSS, including the TSS itself.

Details

This function will only work if the CAGEexp object was built with a BSgenome package, as it needs to extract genomic sequences.

Value

A ggplot2::ggplot object showing the sequence logo. The coordinates displayed are negative for upstream sequences and positive downstream. The position of the TSS is set to 1.

Author(s)

Charles Plessy

See Also

Other CAGEr plot functions: hanabiPlot(), plotAnnot(), plotCorrelation(), plotExpressionProfiles(), plotInterquantileWidth(), plotReverseCumulatives()

Examples

TSSlogo(exampleCAGEexp|>consensusClustersGR(), 20, 10)

charles-plessy/CAGEr documentation built on Aug. 2, 2024, 4:35 p.m.