PING: Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Version 2.20.0

Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.

Browse man pages Browse package API and functions Browse package files

AuthorXuekui Zhang <xuezhang@jhsph.edu>, Raphael Gottardo <raph@stat.ubc.ca>, Sangsoon Woo <swoo@fhcrc.org>
Bioconductor views Clustering Sequencing StatisticalMethod Visualization
Date of publicationNone
MaintainerRenan Sauteraud <rsautera@fhcrc.org>
LicenseArtistic-2.0
Version2.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PING")

Man pages

CoverageTrack: Reads coverage track
NucleosomeTrack: Track for the Nucleosome position
PICS_IMPORT: PICS functions.
PING: Estimation of binding site positions
ping-class: The ping class
pingError-class: The ping class
pingList-class: The ping class
plotSummary: Plot a summary of the prediction for given ranges.
postPING: Post process Estimation of binding site positions obtained...
RawReadsTrack: Raw reads density track
segmentPING: Segment the genome into candidate regions
show: show PING
summary: summary PING

Functions

CoverageTrack Man page Source code
FilterPING Source code
K Man page
K,ping-method Man page
K,pingError-method Man page
K,pingList-method Man page
NucleosomeTrack Man page Source code
PING Man page Source code
PostDelta Source code
PostDup Source code
PostError Source code
PostSigma Source code
RawReadsTrack Man page Source code
[,pingList,ANY,ANY-method Man page
[[,pingList,ANY,ANY-method Man page
as.data.frame,pingList-method Man page
bam2gr Man page
chromosome Man page
chromosome,ping-method Man page
chromosome,pingError-method Man page
chromosome,pingList-method Man page
code Man page
code,ping-method Man page
code,pingError-method Man page
code,pingList-method Man page
coerce Man page
coerce,data.frame,pingList-method Man page Man page
coerce,pingList,RangedData-method Man page
coerce,pingList,data.frame-method Man page
delta Man page
delta,ping-method Man page
delta,pingError-method Man page
delta,pingList-method Man page
density Man page
density,ping-method Man page
density,pingError-method Man page
density,pingList-method Man page
filterPING2 Source code
fitModelAllkSplit Source code
length Man page
length,pingList-method Man page
make.thickthin Source code
makeRangedDataOutput Man page
maxRange Man page
maxRange,ping-method Man page
maxRange,pingError-method Man page
maxRange,pingList-method Man page Man page
minRange Man page
minRange,ping-method Man page
minRange,pingError-method Man page
minRange,pingList-method Man page Man page
mu Man page
mu,ping-method Man page
mu,pingError-method Man page
mu,pingList-method Man page
newPing Man page Source code
newPing,ping-method Man page
newPingError Man page Source code
newPingError,pingError-method Man page
newPingList Man page Source code
newPingList,pingList-method Man page
ping Man page
ping-class Man page
pingError Man page
pingError-class Man page
pingList Man page
pingList-class Man page
plot Man page
plot,data.frame,data.frame-method Man page
plot,ping,segReads-method Man page
plot,pingError,segReads-method Man page
plot,pingList,pingList-method Man page
plot,pingList,segReadsList-method Man page
plotSummary Man page Source code
postPING Man page Source code
processDup Source code
score Man page
score,ping-method Man page
score,pingError-method Man page
score,pingList-method Man page
scoreForward Man page
scoreForward,ping-method Man page
scoreForward,pingError-method Man page
scoreForward,pingList-method Man page
scoreReverse Man page
scoreReverse,ping-method Man page
scoreReverse,pingError-method Man page
scoreReverse,pingList-method Man page
se Man page
se,ping-method Man page
se,pingError-method Man page
se,pingList-method Man page
seF Man page
seF,ping-method Man page
seF,pingError-method Man page
seF,pingList-method Man page
seR Man page
seR,ping-method Man page
seR,pingError-method Man page
seR,pingList-method Man page
segReads Man page
segReadsList Man page
segReadsListPE Man page
segReadsPE Man page
segmentPING Man page Source code
setParaEM Man page
setParaPrior Man page
show Man page
show,ping-method Man page
show,pingError-method Man page
show,pingList-method Man page
show,segReads-method Man page
show,segReadsList-method Man page
show-methods Man page
sigmaSqF Man page
sigmaSqF,ping-method Man page
sigmaSqF,pingError-method Man page
sigmaSqF,pingList-method Man page
sigmaSqR Man page
sigmaSqR,ping-method Man page
sigmaSqR,pingError-method Man page
sigmaSqR,pingList-method Man page
summary Man page
summary,ping-method Man page
summary,pingList-method Man page
summary,segReads-method Man page
summary,segReadsList-method Man page
summary-methods Man page
truncateResult Source code
w Man page
w,ping-method Man page
w,pingError-method Man page
w,pingList-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/PING.R
R/postPING.R
R/segmentPING.R
R/setClasses.R
R/setMethods.R
aclocal.m4
build
build/vignette.rds
cleanup
configure
configure.ac
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/PING-PE.R
inst/doc/PING-PE.Rnw
inst/doc/PING-PE.pdf
inst/doc/PING.R
inst/doc/PING.Rnw
inst/doc/PING.pdf
inst/extdata
inst/extdata/GSM351492_R4_chr1.bed
inst/extdata/yeastChrI.bam
man
man/CoverageTrack.Rd
man/NucleosomeTrack.Rd
man/PICS_IMPORT.Rd
man/PING.Rd
man/RawReadsTrack.Rd
man/ping-class.Rd
man/pingError-class.Rd
man/pingList-class.Rd
man/plotSummary.Rd
man/postPING.Rd
man/segmentPING.Rd
man/show.Rd
man/summary.Rd
src
src/Makevars.in
src/Makevars.win
src/init.c
src/ping.c
src/ping.h
vignettes
vignettes/GPL.txt
vignettes/PING-PE.Rnw
vignettes/PING.Rnw
PING documentation built on May 20, 2017, 10:54 p.m.