GenoGAM: A GAM based framework for analysis of ChIP-Seq data
Version 1.4.0

This package allows statistical analysis of genome-wide data with smooth functions using generalized additive models based on the implementation from the R-package 'mgcv'. It provides methods for the statistical analysis of ChIP-Seq data including inference of protein occupancy, and pointwise and region-wise differential analysis. Estimation of dispersion and smoothing parameters is performed by cross-validation. Scaling of generalized additive model fitting to whole chromosomes is achieved by parallelization over overlapping genomic intervals.

AuthorGeorg Stricker [aut, cre], Alexander Engelhardt [aut], Julien Gagneur [aut]
Bioconductor views ChIPSeq DifferentialExpression DifferentialPeakCalling Epigenetics Genetics Regression
Date of publicationNone
MaintainerGeorg Stricker <georg.stricker@in.tum.de>
LicenseGPL-2
Version1.4.0
URL https://github.com/gstricker/GenoGAM
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GenoGAM")

Popular man pages

dataRange: The /codeGRanges of the underlying data
design: Access the 'design' slot
GenoGAMDataSetToDataFrame: GenoGAMDataSet to DataFrame
GenoGAM-methods: GenoGAM-methods
getCoordinates: Accessor to the /codecoordinates slot
plot.GenoGAM: The pot function for a GenoGAM object
qualityCheck: A function to quality check the data
See all...

All man pages Function index File listing

Man pages

asDataFrame: GenomicTiles to DataFrame
callPeaks: Call peaks on a GenoGAM object
changeSettings: Check data compliance with tile settings
checkSettings: Check data compliance with tile settings
computeRegionSignificance: Compute significance for given regions
computeSignificance: Compute significance.
computeSizeFactors: computeSizeFactors
dataRange: The /codeGRanges of the underlying data
design: Access the 'design' slot
filterData: A filter function for |codeGenoGAMDataSet
fitGenoGAM: genogam
GenoGAM: GenoGAM: A package providing a framework to analyse ChIP-Seq...
GenoGAM-class: GenoGAM class
GenoGAMDataSet: GenoGAMDataSet constructor.
GenoGAMDataSet-brackets: Subsetting by GRanges
GenoGAMDataSet-class: GenoGAMDataSet
GenoGAMDataSetToDataFrame: GenoGAMDataSet to DataFrame
GenoGAM-methods: GenoGAM-methods
GenoGAMSettings: The constructor function for GenoGAMSettings
GenoGAMSettings-class: GenoGAMSettings
GenoGAM-view: View the dataset
GenomicTiles: GenomicTiles constructor.
GenomicTiles-brackets: Providing pseudo-list functionality
GenomicTiles-class: GenomicTiles class
GenomicTiles-metrics: Computing metrics
GenomicTiles-view: View the dataset
getChunkIndex: Compute the index for chunks instead tiles
getCoordinates: Accessor to the /codecoordinates slot
getIndex: Accessor to the 'index' slot
getIndexCoordinates: Compute the row coordinates for a given index
getTile: Tile extraction as a DataFrame
makeTestGenoGAM: Make an example /codeGenoGAM
makeTestGenoGAMDataSet: Make an example /codeGenoGAMDataSet
makeTestGenomicTiles: Make an example /codeGenomicTile
plot.GenoGAM: The pot function for a GenoGAM object
qualityCheck: A function to quality check the data
sizeFactors: Access the 'sizeFactor' slot
subsetByOverlaps-GenoGAM-ANY-method: Subset by overlaps method for 'GenoGAM'
subsetByOverlaps-GenoGAMDataSet-GRanges-method: Subset by overlaps method for 'GenoGAMDataSet'
subsetByOverlaps-GenomicTiles-GRanges-method: Subset by overlaps method for 'GenomciTiles'
subset-GenoGAMDataSet-method: Subset method for 'GenoGAMDataSet'
subset-GenoGAM-method: Subset method for 'GenoGAM'
subset-GenomicTiles-method: Subset method for /codeGenomciTiles
tileSettings: Return tile settings
tileSettings-elements: The single entries of the tile settings
untile: Set index to chunkIndex
writeToBEDFile: Write peaks to BED6+3/4 format

Functions

GenoGAM Man page Source code
GenoGAM-class Man page
GenoGAM-methods Man page
GenoGAMDataSet Man page Source code
GenoGAMDataSet-class Man page
GenoGAMDataSetFromConfig Source code
GenoGAMDataSetFromSE Source code
GenoGAMDataSetToDataFrame Man page Source code
GenoGAMSettings Man page Source code
GenoGAMSettings-class Man page
GenomicTiles Man page Source code
GenomicTiles-class Man page
GenomicTilesFromRawData Source code
GenomicTilesFromSE Source code
GenomicTilesToDataFrame Source code
IQR,GenomicTiles-method Man page
MetricsFun Source code
Summary,GenomicTiles-method Man page
[,GenoGAMDataSet,GRanges,ANY,ANY-method Man page
[,GenomicTiles,GRanges,ANY,ANY-method Man page
[[,GenomicTiles,numeric,ANY-method Man page
asDataFrame Man page
bspline Source code
callBroadPeaks Source code
callPeaks Man page Source code
centerFragments Source code
changeChromosomes Source code
changeChunkSize Source code
changeNumberOfTiles Source code
changeOverhangSize Source code
changeSettings Man page Source code
changeSettings,GenomicTiles,character-method Man page
changeTileSize Source code
checkChromosomes Source code
checkChunkSize Source code
checkGenomicTiles Source code
checkNumberOfTiles Source code
checkOverhangSize Source code
checkSettings Man page Source code
checkSettings,GenomicTiles-method Man page
checkTileSize Source code
chunkBAM Source code
colData,GenoGAM-method Man page
combineTrack Source code
commonSubstring Source code
computeBroadPeakSignificance Source code
computePeakSignificance Source code
computeRegionSignificance Man page Source code
computeSignificance Man page Source code
computeSizeFactors Man page Source code
computeSpline Source code
computeTileExtremes Source code
computeZscore Source code
compute_filter Source code
countFragments Source code
dataRange Man page
dataRange,GPos-method Man page
dataRange,GenomicTiles-method Man page
deseq Source code
design,GenoGAM-method Man page
design,GenoGAMDataSet-method Man page
design<-,GenoGAMDataSet,ANY-method Man page
doCrossValidation Source code
exactSubsetByOverlaps Source code
extractFullGenomicTiles Source code
extractGenomicTilesByBlocks Source code
extractGenomicTilesByIndex Source code
extractSplines Source code
filterData Man page Source code
find_root Source code
genogam Man page Source code
getChromosomes Man page
getChromosomes,GenomicTiles-method Man page
getChunkIndex Man page
getChunkIndex,GenomicTiles-method Man page
getChunkSize Man page
getChunkSize,GenomicTiles-method Man page
getCoordinates Man page
getCoordinates,GenomicTiles-method Man page
getExtremes Source code
getFits Man page
getFits,GenoGAM-method Man page
getFunctions Source code
getIndex Man page
getIndex,GenomicTiles-method Man page
getIndexCoordinates Man page
getIndexCoordinates,GenomicTiles-method Man page
getNumCols Source code
getOverhangSize Man page
getOverhangSize,GenomicTiles-method Man page
getPairedCenters Source code
getTile Man page Source code
getTile,GenomicTiles-method Man page
getTileNumber Man page
getTileNumber,GenomicTiles-method Man page
getTileSize Man page
getTileSize,GenomicTiles-method Man page
getVars Source code
guessFactorGroups Source code
leaveOutConsecutiveIntervals Source code
loglik Source code
mad,GenomicTiles-method Man page
makeCoordinates Source code
makeTestGenoGAM Man page Source code
makeTestGenoGAMDataSet Man page Source code
makeTestGenomicTiles Man page Source code
makeTiles Source code
mean,GenomicTiles-method Man page
median,GenomicTiles-method Man page
meltGTile Source code
mergeRanges Source code
nitCV Source code
normalize Source code
normalizeConfig Source code
parsePeaks Source code
plot.GenoGAM Man page Source code Source code
plotQC_GenoGAMDataSet Source code
plotQC_hist Source code
plot_base Source code
plot_ggplot2 Source code
processCountChunks Source code
pvals Source code
qcGenoGAMDataSet Source code
qualityCheck Man page Source code
readBAM Source code
readBED Source code
readData Source code
readRawData Source code
result Source code
rowRanges,GenoGAM-method Man page
sd,GenomicTiles-method Man page
showGenoGAM Source code
showGenoGAMSettings Source code
showGenomicTiles Source code
sizeFactors,GenoGAMDataSet-method Man page
sizeFactors<-,GenoGAMDataSet,ANY-method Man page
subset,GenoGAM-method Man page
subset,GenoGAMDataSet-method Man page
subset,GenomicTiles-method Man page
subsetByDoubleBrackets Source code
subsetByOverlaps Source code
subsetByOverlaps,GenoGAM,ANY-method Man page
subsetByOverlaps,GenoGAMDataSet,GRanges-method Man page
subsetByOverlaps,GenomicTiles,GRanges-method Man page
subsetByPosition Source code
subsetByRanges Source code
subsetGenomicTiles Source code
subsetGenomicTilesByOverlaps Source code
subsetIndeces Source code
tileSettings Man page
tileSettings,GenomicTiles-method Man page
unlistCoordinates Source code
untile Man page Source code
untile,GenomicTiles-method Man page
updateFormula Source code
validateBAMParamsType Source code
validateCVParamsType Source code
validateChromosomes Source code
validateCoordinatesType Source code
validateDesignType Source code Source code
validateExpDesignType Source code
validateFitParamsType Source code
validateFitsType Source code
validateGenoGAM Source code
validateGenoGAMDataSet Source code
validateGenoGAMSettings Source code
validateGenomicTiles Source code
validateIndexType Source code
validateOptimControlType Source code
validateOptimMethodType Source code
validatePositionsType Source code
validateProcessType Source code
validateSFType Source code
validateSettingsType Source code Source code
validateSmoothsType Source code
validateTileSettingsType Source code
validateVCovType Source code
var,GenomicTiles,ANY-method Man page
view Man page
view,GenoGAM-method Man page
view,GenomicTiles-method Man page
writeToBEDFile Man page Source code
writeToBroadPeaks Source code
writeToNarrowPeaks Source code
xsd Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GenoGAM-class.R
R/GenoGAM-package.R
R/GenoGAMDataSet-class.R
R/GenoGAMSettings-class.R
R/GenomicTiles-class.R
R/cv.R
R/devel.R
R/diffBinding.R
R/filter.R
R/genogam.R
R/helper.R
R/peakCalling.R
R/plotting.R
R/qc.R
R/readData.R
R/sf.R
build
build/vignette.rds
inst
inst/doc
inst/doc/GenoGAM.R
inst/doc/GenoGAM.Rnw
inst/doc/GenoGAM.pdf
inst/extdata
inst/extdata/Set1
inst/extdata/Set1/H3K4ME3_Full_length_Set1_Rep_1_YNL176C.bam
inst/extdata/Set1/H3K4ME3_Full_length_Set1_Rep_1_YNL176C.bam.bai
inst/extdata/Set1/H3K4ME3_Full_length_Set1_Rep_2_YNL176C.bam
inst/extdata/Set1/H3K4ME3_Full_length_Set1_Rep_2_YNL176C.bam.bai
inst/extdata/Set1/H3K4ME3_aa762-1080_Set1_Rep_1_YNL176C.bam
inst/extdata/Set1/H3K4ME3_aa762-1080_Set1_Rep_1_YNL176C.bam.bai
inst/extdata/Set1/H3K4ME3_aa762-1080_Set1_Rep_2_YNL176C.bam
inst/extdata/Set1/H3K4ME3_aa762-1080_Set1_Rep_2_YNL176C.bam.bai
inst/extdata/Set1/README
inst/extdata/Set1/experimentDesign.txt
inst/extdata/Set1/fit.rda
man
man/GenoGAM-class.Rd
man/GenoGAM-methods.Rd
man/GenoGAM-view.Rd
man/GenoGAM.Rd
man/GenoGAMDataSet-brackets.Rd
man/GenoGAMDataSet-class.Rd
man/GenoGAMDataSet.Rd
man/GenoGAMDataSetToDataFrame.Rd
man/GenoGAMSettings-class.Rd
man/GenoGAMSettings.Rd
man/GenomicTiles-brackets.Rd
man/GenomicTiles-class.Rd
man/GenomicTiles-metrics.Rd
man/GenomicTiles-view.Rd
man/GenomicTiles.Rd
man/asDataFrame.Rd
man/callPeaks.Rd
man/changeSettings.Rd
man/checkSettings.Rd
man/computeRegionSignificance.Rd
man/computeSignificance.Rd
man/computeSizeFactors.Rd
man/dataRange.Rd
man/design.Rd
man/filterData.Rd
man/fitGenoGAM.Rd
man/getChunkIndex.Rd
man/getCoordinates.Rd
man/getIndex.Rd
man/getIndexCoordinates.Rd
man/getTile.Rd
man/makeTestGenoGAM.Rd
man/makeTestGenoGAMDataSet.Rd
man/makeTestGenomicTiles.Rd
man/plot.GenoGAM.Rd
man/qualityCheck.Rd
man/sizeFactors.Rd
man/subset-GenoGAM-method.Rd
man/subset-GenoGAMDataSet-method.Rd
man/subset-GenomicTiles-method.Rd
man/subsetByOverlaps-GenoGAM-ANY-method.Rd
man/subsetByOverlaps-GenoGAMDataSet-GRanges-method.Rd
man/subsetByOverlaps-GenomicTiles-GRanges-method.Rd
man/tileSettings-elements.Rd
man/tileSettings.Rd
man/untile.Rd
man/writeToBEDFile.Rd
vignettes
vignettes/GenoGAM.Rnw
vignettes/Overview.png
vignettes/bibliog.bib
vignettes/splines.png
GenoGAM documentation built on May 20, 2017, 10:16 p.m.

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