TssResult-class: Class 'TssResult'

In TSSi: Transcription Start Site Identification

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 <[e-mail]>

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")

Example output

Attaching package: 'TSSi'

The following object is masked from 'package:graphics':

    segments

Class "TssResult" [package "TSSi"]

Slots:
                                                             
Name:         tss      reads   segments parameters annotation
Class:       list       list data.frame       list        ANY

Extends: 
Class "TssNorm", directly
Class "TssData", by class "TssNorm", distance 2

TSSi documentation built on May 6, 2019, 2:40 a.m.