Ringo: R Investigation of ChIP-chip Oligoarrays

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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.

Author
Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber
Date of publication
None
Maintainer
J. Toedling <jtoedling@yahoo.de>
License
Artistic-2.0
Version
1.38.0

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