Class TssResult

Description

Class TssResult storing final sequence read data with identified TSS.

Slots

reads:

List with the read data for each segment.

segments:

Data frame with the information of the individual segments.

tss:

List of the identified TSS locations.

annotation:

Annotation data object, as passed through the annotation argument.

parameters:

List with the parameters.

Methods

All methods for class TssNorm, as well as:

identify methods:

identifyStartSites:

signature(x="TssNorm")

Identify TSS in the normalized data.

get methods:

expect:

signature(x="TssResult")

Get the expectation for non-specific reads, seestart.

tss:

signature(x="TssResult")

Get the identified transcription start sites, seestart.

[:

signature(x="TssResult")

Subset the object, by name or index.

asRangedData methods:

tssAsRangedData:

signature(x="TssResult")

Convert the tss predictions, as obtained by the tss method, to an object of class RangedData.

Author(s)

Maintainer: Julian Gehring <julian.gehring@fdm.uni-freiburg.de>

See Also

Classes: TssData, TssNorm, TssResult

Methods: segmentizeCounts, normalizeCounts, identifyStartSites, get-methods, plot-methods, asRangedData-methods

Functions: subtract-functions

Data set: physcoCounts

Package: TSSi-package

Examples

showClass("TssResult")