pics-class: PICS class

In PICS: Probabilistic inference of ChIP-seq

Description

This object is used to gather all parameters from fitting PICS to a single candidate region.

Usage

## S4 method for signature 'pics'
show(object)

## S4 method for signature 'pics'
minRange(x)

## S4 method for signature 'pics'
maxRange(x)

## S4 method for signature 'pics'
score(x)

## S4 method for signature 'pics'
scoreReverse(x)

## S4 method for signature 'pics'
scoreForward(x)

## S4 method for signature 'pics'
chromosome(x)

## S4 method for signature 'pics'
se(x)

## S4 method for signature 'pics'
seF(x)

## S4 method for signature 'pics'
seR(x)

## S4 method for signature 'pics'
sigmaSqF(x)

## S4 method for signature 'pics'
sigmaSqR(x)

## S4 method for signature 'pics'
delta(x)

## S4 method for signature 'pics'
mu(x)

## S4 method for signature 'pics'
w(x)

## S4 method for signature 'pics'
K(x)

## S4 method for signature 'pics'
code(x)

## S4 method for signature 'pics'
summary(object)

Arguments

object, x

A pics object.

Functions

• show,pics-method: show method

• minRange,pics-method: Get start of range

• maxRange,pics-method: Get end of range

• score,pics-method: Score accessor.

• scoreReverse,pics-method: Reverse score accessor.

• scoreForward,pics-method: Forward score accessor.

• chromosome,pics-method: Chromosome accessor

• se,pics-method: se accessor

• seF,pics-method: Forward se accessor

• seR,pics-method: Reverse se accessor

• sigmaSqF,pics-method: sigmaSqF accessor

• sigmaSqR,pics-method: sigmaSqR accessor

• delta,pics-method: delta accessor

• mu,pics-method: mu accessor

• w,pics-method: w accessor

• K,pics-method: K accessor

• code,pics-method: Error code accessor

• summary,pics-method: Summary of the object

Slots

estimates

A list containing all parameters estimates as well as standard errors.

Nmerged

The number of binding events that were merged; binding events that overlap are merged.

converge

A logical value indicating whether the EM algorithm has converged.

chr

The candidate region's chromosome.

score

Score of the binding event

scoreF

Forward score of the binding event.

scoreR

Reverse score of the binding event.

range

Genomic ranges.

PICS documentation built on Nov. 8, 2020, 8:21 p.m.