# Probabilistic inference of ChIP-seq

## Documentation for package ‘PICS’ version 2.4.1

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

## Help Pages

A B C D F K L M N P S W misc

## -- A --

as.list-method | Estimation of binding site positions

## -- B --

bam2gr | pre-process bam files

## -- C --

candidate.region | Segmentation of paired-end sequencing data
chromosome | The pics class
chromosome-method | The pics class
chromosome-method | The pics class
chromosome-method | The pics class
code | Estimation of binding site positions
code-method | Estimation of binding site positions
coerce | Estimation of binding site positions
coerce-method | Estimation of binding site positions

## -- D --

delta | The pics class
delta-method | The pics class
delta-method | The pics class
delta-method | The pics class
density-method | The pics class

## -- F --

FDR | FDR plot for PICS

## -- K --

K | Estimation of binding site positions
K-method | Estimation of binding site positions

## -- L --

length | The pics class
length-method | Segment the genome into candidate regions
length-method | The pics class

## -- M --

makeRangedDataOutput | Create a RangedData object from a PICS output
map | Segment the genome into candidate regions
map-method | Segment the genome into candidate regions
maxRange | Estimation of binding site positions
maxRange-method | Estimation of binding site positions
minRange | Estimation of binding site positions
minRange-method | Estimation of binding site positions
mu | The pics class
mu-method | The pics class
mu-method | The pics class
mu-method | The pics class

## -- N --

newPics | The pics class
newPics-method | The pics class
newPicsError | The pics class
newPicsError-method | The pics class
newPicsList | The pics class
newPicsList-method | The pics class

## -- P --

PICS | Estimation of binding site positions
pics | Estimation of binding site positions
pics-class | Estimation of binding site positions
picsError | The pics class
picsError-class | The pics class
picsFDR | Estimate the FDR.
picsList | The pics class
picsList-class | The pics class
plot-method | Estimation of binding site positions
plot-method | FDR plot for PICS

## -- S --

score | Estimation of binding site positions
score-method | The pics class
score-method | The pics class
score-method | The pics class
scoreForward | Estimation of binding site positions
scoreForward-method | Estimation of binding site positions
scoreReverse | Estimation of binding site positions
scoreReverse-method | Estimation of binding site positions
se | The pics class
se-method | The pics class
se-method | The pics class
se-method | The pics class
seF | The pics class
seF-method | The pics class
seF-method | The pics class
seF-method | The pics class
segChrRead | Segmentation of paired-end sequencing data
segmentPICS | Segment the genome into candidate regions
segReads | Segment the genome into candidate regions
segReads-class | Segment the genome into candidate regions
segReadsGeneric | Segment the genome into candidate regions
segReadsList | Segment the genome into candidate regions
segReadsList-class | Segment the genome into candidate regions
segReadsListPE | List of segReadsPE objects
segReadsListPE-class | List of segReadsPE objects
segReadsPE | Class to store post-segmentation result
segReadsPE-class | Class to store post-segmentation result
seR | The pics class
seR-method | The pics class
seR-method | The pics class
seR-method | The pics class
setParaEM | Function that returns a list of parameters for the EM algorithm that can be used as an argument of PICS.
setParaPrior | Function that returns a list of parameters that can be used as an argument of PICS.
show | show PICS
show-method | show PICS
show-methods | show PICS
sigmaSqF | Estimation of binding site positions
sigmaSqF-method | Estimation of binding site positions
sigmaSqR | Estimation of binding site positions
sigmaSqR-method | Estimation of binding site positions
summary | summary PICS
summary-method | summary PICS
summary-methods | summary PICS
summarySeg | Summarize a segReadsList object.

## -- W --

w | The pics class
w-method | The pics class
w-method | The pics class
w-method | The pics class
wigDensity | Estimation of binding site positions
wigDensity-method | Estimation of binding site positions

## -- misc --

%in%-method | Segment the genome into candidate regions
[-method | Segment the genome into candidate regions
[-method | The pics class
[-method | List of segReadsPE objects
[[-method | Segment the genome into candidate regions
[[-method | The pics class
[[-method | List of segReadsPE objects