TssData-class: Class 'TssData'

In TSSi: Transcription Start Site Identification

Description

Class TssData storing raw sequence read data.

Slots

reads:

List with the read data for each segment.

segments:

Data frame with the information of the individual segments.

parameters:

List with parameters used for the analysis.

annotation:

Annotation data object, as passed through the annotation argument.

Methods

segmentizeCounts methods:

segmentizeCounts:

signature(nReads="integer", start="integer")

Import raw data and divide into segments.

plot method:

plot:

signature(x="TssData", y="ANY")

Visualize the data.

get methods:

start:

signature(x="TssData")

Get the read start sites. The second argument selects the individual segment; if missing returns a list containing the information of all segments.

end:

signature(x="TssData")

Get the read end sites, see start.

counts:

signature(x="TssData")

Get the raw read counts, see start.

reads:

signature(x="TssData")

Get all the read data of the segments, including e.g. ‘start’, ‘counts’, ‘replicate’, , see start.

segments:

signature(x="TssData")

Get the information associated with the segments, e.g. chromosome, strand, region. The second and third argument select the segment and the variable of interest.

parameters:

signature(x="TssData")

Get the parameters used in the analysis.

annotation:

signature(x="TssData")

Get the annotation data, as passed through the annotation argument.

[:

signature(x="TssData")

Subset the object, by name or index.

show methods:

show:

signature(object="TssData")

asRangedData methods:

readsAsRangedData:

signature(x="TssData")

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

segmentsAsRangedData:

signature(x="TssData")

Convert the segments, as obtained by the segments 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("TssData")

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