Probabilistic inference of ChIP-seq


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Documentation for package ‘PICS’ version 2.28.0

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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