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

## Documentation for package ‘PING’ version 1.0.0

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

## Help Pages

%in%-method | Segment the genome into candidate regions
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
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 | Segment the genome into candidate regions
length-method | The ping class
makeRangedDataOutput | Create a RangedData object from a PING 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 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
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
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
postPING | Post process Estimation of binding site positions obtained from PING
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
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 ping class
seR-method | The ping class
seR-method | The ping class
seR-method | The ping class
setParaEM | Set convergence parameters of the EM algorithm
setParaPrior | Set convergence parameters of the EM algorithm
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
unique | GenomeData Unique Reads
unique-method | GenomeData Unique Reads
unique-methods | GenomeData Unique Reads
w | The ping class
w-method | The ping class
w-method | The ping class
w-method | The ping class
[-method | Segment the genome into candidate regions
[-method | The ping class
[[-method | Segment the genome into candidate regions
[[-method | The ping class