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


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Documentation for package ‘PING’ version 1.0.0

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%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