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

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]
Date of publicationNone
MaintainerGeorg Stricker <georg.stricker@in.tum.de>
LicenseGPL-2
Version1.2.1
https://github.com/gstricker/GenoGAM

View on Bioconductor

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

asDataFrame Man page
callPeaks Man page
changeSettings Man page
changeSettings,GenomicTiles,character-method Man page
checkSettings Man page
checkSettings,GenomicTiles-method Man page
colData,GenoGAM-method Man page
computeRegionSignificance Man page
computeSignificance Man page
computeSizeFactors Man page
dataRange Man page
dataRange,GenomicTiles-method Man page
dataRange,GPos-method Man page
design<-,GenoGAMDataSet,ANY-method Man page
design,GenoGAMDataSet-method Man page
design,GenoGAM-method Man page
filterData Man page
genogam Man page
GenoGAM Man page
GenoGAM-class Man page
GenoGAMDataSet Man page
GenoGAMDataSet-class Man page
[,GenoGAMDataSet,GRanges,ANY,ANY-method Man page
GenoGAMDataSetToDataFrame Man page
GenoGAM-methods Man page
GenoGAMSettings Man page
GenoGAMSettings-class Man page
GenomicTiles Man page
GenomicTiles-class Man page
[,GenomicTiles,GRanges,ANY,ANY-method Man page
[[,GenomicTiles,numeric,ANY-method Man page
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
getFits Man page
getFits,GenoGAM-method Man page
getIndex Man page
getIndexCoordinates Man page
getIndexCoordinates,GenomicTiles-method Man page
getIndex,GenomicTiles-method Man page
getOverhangSize Man page
getOverhangSize,GenomicTiles-method Man page
getTile Man page
getTile,GenomicTiles-method Man page
getTileNumber Man page
getTileNumber,GenomicTiles-method Man page
getTileSize Man page
getTileSize,GenomicTiles-method Man page
IQR,GenomicTiles-method Man page
mad,GenomicTiles-method Man page
makeTestGenoGAM Man page
makeTestGenoGAMDataSet Man page
makeTestGenomicTiles Man page
mean,GenomicTiles-method Man page
median,GenomicTiles-method Man page
plot.GenoGAM Man page
qualityCheck Man page
rowRanges,GenoGAM-method Man page
sd,GenomicTiles-method Man page
sizeFactors<-,GenoGAMDataSet,ANY-method Man page
sizeFactors,GenoGAMDataSet-method Man page
subsetByOverlaps,GenoGAM,ANY-method Man page
subsetByOverlaps,GenoGAMDataSet,GRanges-method Man page
subsetByOverlaps,GenomicTiles,GRanges-method Man page
subset,GenoGAMDataSet-method Man page
subset,GenoGAM-method Man page
subset,GenomicTiles-method Man page
Summary,GenomicTiles-method Man page
tileSettings Man page
tileSettings,GenomicTiles-method Man page
untile Man page
untile,GenomicTiles-method Man page
var,GenomicTiles,ANY-method Man page
view Man page
view,GenoGAM-method Man page
view,GenomicTiles-method Man page
writeToBEDFile Man page

Files

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

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