Get methods

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Description

Get methods for objects of the classes TssData, TssNorm, and TssResult.

Value

A data frame or list

Methods

For class TssData, TssNorm (inherited), TssResult (inherited):

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(object="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 optional second and third arguments select the segment and the variable of interest.

annotation:

signature(x="TssData")

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

[:

signature(x="TssData")

Subset the object, by name or index.

For class TssNorm, TssResult (inherited):

ratio:

signature(x="TssNorm")

Get the normalized reads based on the Poisson ratios; see start.

fit:

signature(x="TssNorm")

Get the normalized reads based on the fit; see start.

For class TssResult:

expect:

signature(x="TssResult")

Get the expectation for non-specific reads; see start.

tss:

signature(x="TssResult")

Get the identified transcription start sites; see start.

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

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example(segmentizeCounts)

## some examples for get methods
start(x)
head(start(x, 1))

head(reads(x, 1))

segments(x)
names(x)