# Probabilistic inference of ChIP-seq

## Documentation for package ‘PICS’ version 2.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

B C D K L M P S W misc

## -- B --

bam2gr | Pre-process bam files

## -- C --

candidate.region | Identify candidate regions
chromosome | Generics associated with pics classes
chromosome-method | PICS class
chromosome-method | Generics associated with pics classes
chromosome-method | picsError class
chromosome-method | List of PICS objects
code | Generics associated with pics classes
code-method | PICS class
code-method | picsError class
code-method | List of PICS objects

## -- D --

delta | Generics associated with pics classes
delta-method | PICS class
delta-method | Generics associated with pics classes
delta-method | picsError class
delta-method | List of PICS objects

## -- K --

K | Generics associated with pics classes
K-method | PICS class
K-method | picsError class
K-method | List of PICS objects

## -- L --

length-method | List of PICS objects
length-method | Classes and functions to segment the genome in candidate regions

## -- M --

makeGRangesOutput | Export a PICS object to GRanges
map | Classes and functions to segment the genome in candidate regions
map-method | Classes and functions to segment the genome in candidate regions
maxRange | Generics associated with pics classes
maxRange-method | PICS class
maxRange-method | picsError class
maxRange-method | List of PICS objects
minRange | Generics associated with pics classes
minRange-method | PICS class
minRange-method | picsError class
minRange-method | List of PICS objects
mu | Generics associated with pics classes
mu-method | PICS class
mu-method | Generics associated with pics classes
mu-method | picsError class
mu-method | List of PICS objects

## -- P --

PICS | Estimation of binding site positions
pics-class | PICS class
pics-generics | Generics associated with pics classes
picsError-class | picsError class
picsFDR | Estimate the FDR
picsList-class | List of PICS objects
plot-FDR | Plot PICS FDR
plot-method | Plot PICS FDR
plot-method | Plot methods for PICS objects
plot-pics | Plot methods for PICS objects

## -- S --

score | Generics associated with pics classes
score-method | PICS class
score-method | Generics associated with pics classes
score-method | picsError class
score-method | List of PICS objects
scoreForward | Generics associated with pics classes
scoreForward-method | PICS class
scoreForward-method | Generics associated with pics classes
scoreForward-method | picsError class
scoreForward-method | List of PICS objects
scoreReverse | Generics associated with pics classes
scoreReverse-method | PICS class
scoreReverse-method | Generics associated with pics classes
scoreReverse-method | picsError class
scoreReverse-method | List of PICS objects
se | Generics associated with pics classes
se-method | PICS class
se-method | Generics associated with pics classes
se-method | picsError class
se-method | List of PICS objects
seF | Generics associated with pics classes
seF-method | PICS class
seF-method | Generics associated with pics classes
seF-method | picsError class
seF-method | List of PICS objects
segChrRead | Segmentation of paired-end sequencing data
segmentPICS | Segment the genome into candidate regions
segReads | Classes and functions to segment the genome in candidate regions
segReads-class | Classes and functions to segment the genome in candidate regions
segReadsGeneric | Perform genome segmentation depending
segReadsList | Classes and functions to segment the genome in candidate regions
segReadsList-class | Classes and functions to segment the genome in candidate regions
segReadsListPE | Class and methods for list of candidate regions from paired-end data
segReadsListPE-class | Class and methods for list of candidate regions from paired-end data
segReadsPE | Classe and methods for candidate regions from paired-end data
segReadsPE-class | Classe and methods for candidate regions from paired-end data
seR | Generics associated with pics classes
seR-method | PICS class
seR-method | Generics associated with pics classes
seR-method | picsError class
seR-method | List of PICS objects
setParaEM | List of parameters for the EM algorithm that can be used as an argument of PICS.
setParaPrior | List of parameters that can be used as an argument of PICS.
show-method | PICS class
show-method | picsError class
show-method | List of PICS objects
show-method | Classes and functions to segment the genome in candidate regions
sigmaSqF | Generics associated with pics classes
sigmaSqF-method | PICS class
sigmaSqF-method | Generics associated with pics classes
sigmaSqF-method | picsError class
sigmaSqF-method | List of PICS objects
sigmaSqR | Generics associated with pics classes
sigmaSqR-method | PICS class
sigmaSqR-method | Generics associated with pics classes
sigmaSqR-method | picsError class
sigmaSqR-method | List of PICS objects
summary-method | PICS class
summary-method | List of PICS objects
summary-method | Classes and functions to segment the genome in candidate regions
summarySeg | Summarize segmentList objects

## -- W --

w | Generics associated with pics classes
w-method | PICS class
w-method | picsError class
w-method | List of PICS objects

## -- misc --

[-method | List of PICS objects
[-method | Classes and functions to segment the genome in candidate regions
[-method | Class and methods for list of candidate regions from paired-end data
[[-method | List of PICS objects
[[-method | Classes and functions to segment the genome in candidate regions
[[-method | Class and methods for list of candidate regions from paired-end data