accessors {segmenter}R Documentation

Accessors for the segmentation objects

Description

These functions can be used to access the contents of segmentation objects as well as modifying them.

Usage

model(object)

## S4 method for signature 'segmentation'
model(object)

emission(object)

## S4 method for signature 'segmentation'
emission(object)

transition(object)

## S4 method for signature 'segmentation'
transition(object)

overlap(object, ...)

## S4 method for signature 'segmentation'
overlap(object, cell)

TSS(object, ...)

## S4 method for signature 'segmentation'
TSS(object, cell)

TES(object, ...)

## S4 method for signature 'segmentation'
TES(object, cell)

segment(object, ...)

## S4 method for signature 'segmentation'
segment(object, cell)

bins(object, ...)

## S4 method for signature 'segmentation'
bins(object, cell)

counts(object, ...)

## S4 method for signature 'segmentation'
counts(object, cell)

likelihood(object)

## S4 method for signature 'segmentation'
likelihood(object)

cells(object)

## S4 method for signature 'segmentation'
cells(object)

states(object)

## S4 method for signature 'segmentation'
states(object)

markers(object)

## S4 method for signature 'segmentation'
markers(object)

Arguments

object

An object of class segmentation

...

Other argument passed to the accessors

cell

A string

Value

The data in the corresponding slot or a subset of it.

See Also

segmentation

Examples

model(test_obj)

emission(test_obj)

transition(test_obj)

overlap(test_obj)
overlap(test_obj, cell = 'K562')

TSS(test_obj)
TSS(test_obj, cell = 'K562')

TES(test_obj)
TES(test_obj, cell = 'K562')

segment(test_obj)
segment(test_obj, cell = 'K562')

bins(test_obj)

counts(test_obj)

likelihood(test_obj)

cells(test_obj)

states(test_obj)

markers(test_obj)


[Package segmenter version 1.0.0 Index]