Probabilistic inference of ChIP-seq

Documentation for package ‘PICS’ version 2.37.0

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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