Probabilistic inference of ChIP-seq

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Documentation for package ‘PICS’ version 1.6.0

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

-- A --

as.list-method Estimation of binding site positions

-- C --

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 Estimation of binding site positions
density-method Estimation of binding site positions
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 --

paraEMH Set convergence parameters of the EM algorithm
paraEMTF Set convergence parameters of the EM algorithm
paraPriorH Set convergence parameters of the EM algorithm
paraPriorTF Set convergence parameters of the EM algorithm
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 Compute the global 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
segmentReads Segment the genome into candidate regions
segReads Segment the genome into candidate regions
segReads-class Segment the genome into candidate regions
segReadsList Segment the genome into candidate regions
segReadsList-class Segment the genome into candidate regions
seR The pics class
seR-method The pics class
seR-method The pics class
seR-method The pics class
setParaEM Set convergence parameters of the EM algorithm
setParaPrior Set convergence parameters of the EM algorithm
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

-- U --

unique GenomeData Unique Reads
unique-method GenomeData Unique Reads
unique-methods GenomeData Unique Reads

-- W --

w The pics class
w-method The pics class
w-method The pics class
w-method The pics class

-- misc --

%in%-method Segment the genome into candidate regions
[-method Segment the genome into candidate regions
[-method The pics class
[[-method Segment the genome into candidate regions
[[-method The pics class