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

## Documentation for package ‘PING’ version 2.2.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

bam2gr | pre-process bam files
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
yeast_chrM | Data sets
[-method | The ping class
[[-method | The ping class