Ringo: R Investigation of ChIP-chip Oligoarrays

The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList (raw) or ExpressionSet (pre- processed). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP-chip-specific and NimbleGen-specific functionalities.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Ringo")
AuthorJoern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber
Bioconductor views DataImport Microarray Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerJ. Toedling <jtoedling@yahoo.de>
LicenseArtistic-2.0
Version1.40.0

View on Bioconductor

Man pages

arrayImage: Function to visualize spatial distribution of raw intensities

asExprSet: converts a Ringo MAList into an ExpressionSet

autocorr: Function to compute auto-correlation of probe intensities

cherByThreshold: Function to identify chers based on thresholds

cherClass: Class "cher" - ChIP-enriched region

chipAlongChrom: Visualize ChIP intensities along the chromosome

chipAlongChromOld: Visualize ChIP intensities along the chromosome

compute_gc: Compute the GC content of DNA and probe sequences

computeRunningMedians: Function to compute running medians on a tiling expression...

compute_sliding_t: Function to compute sliding T statistics on a tiling...

corrPlot: Function to plot correlation of different samples

exportCherList: Function to export cherList into a file

extractProbeAnno: Build probeAnno from match positions in an RGList

features2Probes: Function for mapping genomic features to probes

findChersOnSmoothed: Find ChIP-enriched regions on smoothed ExpressionSet

ftr2xys: Convert a NimbleScan ftr-file into a xys-file

getFeats: Utility function to extract all features from a cherList

newCER: Create a list object of class cher

nimblegenNorm: Function to compute scaled log-ratios

nonzero: Methods for Function nonzero

plotAutocorr: Plots auto-correlation of probe intensities

plotBM: Visualization of a binary matrix

plot_cher: Plot identified Chers

posToProbeAnnoEnvironment: Function for creating a probeAnno environment

preprocess: Preprocess Raw ChIP-chip Intensities

probeAnnoClass: Class "probeAnno"

qopS4: Class "qop" Quantiles Over Positions

quantilesOverPositions: show ChIP-chip data aligned over genome features, e.g. TSSs

readNimblegen: Function to read in Nimblegen Intensity Text Files

regionoverlap: Function to compute overlap of genomic regions

relateCERs: Relate found Chers to genomic features

Ringo-internal: Internal Ringo functions

sigGOTable: Obtain significant GO terms for a list of genes

sliding_meansd: Compute mean and standard deviation of scores in a sliding...

sliding_quantile: Compute quantile of scores in a sliding window

twoGaussiansNull: Estimate a threshold from Gaussian mixture distribution

upperBoundNull: function to estimate upper limit of null distribution

validProbeAnno: Function to check a probeAnno environment

Functions

alongChromTicks Man page
arrayImage Man page
arrayName Man page
arrayName<- Man page
arrayName<-,probeAnno,character-method Man page
arrayName,probeAnno-method Man page
as.data.frame.cherList Man page
asExpressionSet Man page
asExprSet Man page
autocor Man page
autocorr Man page
autocorrelation Man page
cbind2,ExpressionSet,ExpressionSet-method Man page
cellType Man page
cellType<- Man page
cellType<-,cher,character-method Man page
cellType,cher-method Man page
cher Man page
Cher Man page
cherByThreshold Man page
cher-class Man page
cherList Man page
cherList-class Man page
cherPlot Man page
chersToBED Man page
chipAlongChrom Man page
chipAlongChrom1 Man page
chipAlongChromOld Man page
chromosomeNames Man page
chromosomeNames,probeAnno-method Man page
clusters Man page
coerce,environment,probeAnno-method Man page
compute.gc Man page
computeRunningMedians Man page
computeSlidingT Man page
corPlot Man page
corrPlot Man page
createProbeAnno Man page
exportCCData Man page
exportCherList Man page
extractProbeAnno Man page
featureColors Man page
featureColors Man page
features2Probes Man page
findChersOnSmoothed Man page
ftr2xys Man page
gccontent Man page
genome Man page
genome<- Man page
genome<-,probeAnno,character-method Man page
genome,probeAnno-method Man page
get,character,missing,probeAnno-method Man page
getFeats Man page
getFeatures Man page
image.RGList Man page
image,RGList-method Man page
initialize,cher-method Man page
initialize,probeAnno-method Man page
ls,probeAnno,missing,missing,missing,missing-method Man page
merge.RGList Man page
newCher Man page
newVP Man page
nimblegenScale Man page
nonzero Man page
nonzero,dgCMatrix-method Man page
nonzero,matrix.csr-method Man page
nonzero,matrix-method Man page
nonzero-methods Man page
normalizeBetweenArraysVSN Man page
nullUpperBound Man page
oneChannelVSN Man page
pair2xys Man page
panel.cor Man page
panel.scatter Man page
plotAlongChromLegend Man page
plotAutocor Man page
plot.autocor.result Man page
plotBinaryMatrix Man page
plotBM Man page
plot.cher Man page
plotCher Man page
plot,cher,ExpressionSet-method Man page
plot,cher,missing-method Man page
plot,ExpressionSet,probeAnno-method Man page
plotOneChIPSample Man page
plot,qop,ANY-method Man page
plot,qop-method Man page
posToProbeAnno Man page
posToProbeAnnoEnvironment Man page
preprocess Man page
probeAnno Man page
[<-,probeAnno,ANY,ANY,ANY-method Man page
[,probeAnno,ANY,ANY,ANY-method Man page
probeAnno-class Man page
probeAnnoFromRGList Man page
[<-,probeAnno-method Man page
[,probeAnno-method Man page
probes Man page
probes,cherList-method Man page
probes,cher-method Man page
qop-class Man page
quantilesOverPositions Man page
readNgIntensitiesTxt Man page
readNimblegen Man page
readNimblegenHeader Man page
region.overlap Man page
regionOverlap Man page
relateChers Man page
relateChers2 Man page
show,cher-method Man page
show,probeAnno-method Man page
show,qop-method Man page
sigGOTable Man page
sliding.meansd Man page
slidingquantile Man page
sliding.quantile Man page
splitAndSimplify Man page
takeMeanOverGroups Man page
twoGaussiansNull Man page
update,cher-method Man page
upperBoundNull Man page
validateProbeAnno Man page
validProbeAnno Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R R/Class_cher.R R/Class_probeAnno.R R/arrayImage.R R/autocorr.R R/cerFinding.R R/chipAlongChrom.R R/chipAlongChrom1.R R/computeSlidingT.R R/corrPlot.R R/enrichedregion.R R/exportTracks.R R/mmeansd.R R/plotBinaryMatrix.R R/preprocess.R R/probeAnnoFunctions.R R/quantilesOverPositions.R R/readNimblegen.R R/regionoverlap.R R/runningMedian.R R/sigGOTable.R R/sparse.R R/twoGaussianNull.R R/upperBoundNull.R R/util.R R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/agilentData
inst/agilentData/H3K4Me3_Tc1Liver_sol1_mmChr17_part.txt
inst/agilentData/arrayDescriptionAMEXP1029_part.txt
inst/agilentData/mm9chr17.RData
inst/agilentData/targets.txt
inst/doc
inst/doc/Ringo.R
inst/doc/Ringo.Rnw
inst/doc/Ringo.pdf
inst/exData
inst/exData/MOD_2003-12-05_SUZ12_1in2.ndf
inst/exData/MOD_2003-12-05_SUZ12_1in2.pos
inst/exData/MOD_20551_PMT1_pair.txt
inst/exData/MOD_20742_PMT1_pair.txt
inst/exData/README.txt
inst/exData/exampleProbeAnno.rda
inst/exData/exampleX.rda
inst/exData/example_targets.txt
inst/exData/reportersInexactMatchesHg18.rda
inst/exData/spottypes.txt
inst/scripts
inst/scripts/condenseBlatOutput.pl
inst/scripts/condenseExonerateOutput.pl
inst/scripts/condenseMUMmerOutput.pl
inst/scripts/convertSampleKeyTxt.R
inst/scripts/extractProbeSequenceFasta.pl
inst/scripts/graphChers2Transcripts.R inst/scripts/makeProbeAnno.R inst/scripts/mapReportersWithBiostrings.R inst/scripts/retrieveGenomicFeatureAnnotation.R
man
man/Ringo-internal.Rd man/arrayImage.Rd man/asExprSet.Rd man/autocorr.Rd man/cherByThreshold.Rd man/cherClass.Rd man/chipAlongChrom.Rd man/chipAlongChromOld.Rd man/computeRunningMedians.Rd man/compute_gc.Rd man/compute_sliding_t.Rd man/corrPlot.Rd man/exportCherList.Rd man/extractProbeAnno.Rd man/features2Probes.Rd man/findChersOnSmoothed.Rd man/ftr2xys.Rd man/getFeats.Rd man/newCER.Rd man/nimblegenNorm.Rd man/nonzero.Rd man/plotAutocorr.Rd man/plotBM.Rd man/plot_cher.Rd man/posToProbeAnnoEnvironment.Rd man/preprocess.Rd man/probeAnnoClass.Rd man/qopS4.Rd man/quantilesOverPositions.Rd man/readNimblegen.Rd man/regionoverlap.Rd man/relateCERs.Rd man/sigGOTable.Rd man/sliding_meansd.Rd man/sliding_quantile.Rd man/twoGaussiansNull.Rd man/upperBoundNull.Rd man/validProbeAnno.Rd
src
src/mmeansd.cpp
src/mmedian.cpp
src/region_overlap.c
src/ringo.h
src/ringo_init.c
vignettes
vignettes/Makefile
vignettes/Ringo-Bibliography.bib
vignettes/Ringo.Rnw
vignettes/Ringo.tex

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