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.

Author
Georg Stricker [aut, cre], Alexander Engelhardt [aut], Julien Gagneur [aut]
Date of publication
None
Maintainer
Georg Stricker <georg.stricker@in.tum.de>
License
GPL-2
Version
1.2.1
URLs

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

Files in this package

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