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.

AuthorJoern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber
Date of publicationNone
MaintainerJ. Toedling <jtoedling@yahoo.de>
LicenseArtistic-2.0
Version1.38.0

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

Files in this package

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

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