Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data

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Documentation for package ‘PING’ version 2.20.0

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as.data.frame-method The ping class
bam2gr PICS functions.
chromosome The ping class
chromosome-method The ping class
chromosome-method The ping class
chromosome-method The ping 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
CoverageTrack Reads coverage track
delta The ping class
delta-method The ping class
delta-method The ping class
delta-method The ping class
density Estimation of binding site positions
density-method Estimation of binding site positions
density-method The ping class
K Estimation of binding site positions
K-method Estimation of binding site positions
length The ping class
length-method The ping class
makeRangedDataOutput PICS functions.
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 ping class
mu-method The ping class
mu-method The ping class
mu-method The ping class
newPing The ping class
newPing-method The ping class
newPingError The ping class
newPingError-method The ping class
newPingList The ping class
newPingList-method The ping class
NucleosomeTrack Track for the Nucleosome position
PING Estimation of binding site positions
ping Estimation of binding site positions
ping-class Estimation of binding site positions
pingError The ping class
pingError-class The ping class
pingList The ping class
pingList-class The ping class
plot Estimation of binding site positions
plot-method Estimation of binding site positions
plotSummary Plot a summary of the prediction for given ranges.
postPING Post process Estimation of binding site positions obtained from PING
RawReadsTrack Raw reads density track
score Estimation of binding site positions
score-method The ping class
score-method The ping class
score-method The ping 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 ping class
se-method The ping class
se-method The ping class
se-method The ping class
seF The ping class
seF-method The ping class
seF-method The ping class
seF-method The ping class
segmentPING Segment the genome into candidate regions
segReads PICS functions.
segReadsList PICS functions.
segReadsListPE PICS functions.
segReadsPE PICS functions.
seR The ping class
seR-method The ping class
seR-method The ping class
seR-method The ping class
setParaEM PICS functions.
setParaPrior PICS functions.
show show PING
show-method show PING
show-methods show PING
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 PING
summary-method summary PING
summary-methods summary PING
w The ping class
w-method The ping class
w-method The ping class
w-method The ping class
[-method The ping class
[[-method The ping class