# A GAM based framework for analysis of ChIP-Seq data

## Documentation for package ‘GenoGAM’ version 2.11.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G I L M N P R S T V W misc

GenoGAM-package | GenoGAM: A package providing a framework to analyse ChIP-Seq data

## -- A --

asCoordinates | IRanges to Coordinates
assay-method | GenoGAM class
assay-method | GenoGAMDataSetList
assay-method | GenoGAMList class
assays-method | GenoGAMDataSetList
assays-method | GenoGAMList class

## -- C --

callPeaks | Call peaks on a GenoGAM object
colData | GenoGAM class
colData-method | GenoGAM class
colData-method | GenoGAMDataSetList
colData-method | GenoGAMList class
colnames | GenoGAM class
colnames-method | GenoGAM class
colnames-method | GenoGAMDataSetList
colnames-method | GenoGAMList class
computeRegionSignificance | Compute significance for given regions
computeSignificance | computeSignificance
computeSizeFactors | computeSizeFactors
Coordinates | Coordinates class
Coordinates-class | Coordinates class

## -- D --

dataRange | GenoGAMDataSet
dataRange-method | GenoGAMDataSet
dataRange-method | GenoGAMDataSetList
design-method | GenoGAM class
design-method | GenoGAMDataSet
design-method | GenoGAMDataSetList
design-method | GenoGAMList class
design<--method | GenoGAMDataSet
design<--method | GenoGAMDataSetList
dim-method | GenoGAMDataSetList
dim-method | GenoGAMList class
dimnames | GenoGAM class
dimnames-method | GenoGAM class
dimnames-method | GenoGAMList class

## -- E --

end-method | Coordinates class
end<--method | Coordinates class

## -- F --

fits | GenoGAM class
fits-method | GenoGAM class
fits-method | GenoGAMList class

## -- G --

GenoGAM | GenoGAM class
GenoGAM | GenoGAM: A package providing a framework to analyse ChIP-Seq data
genogam | genogam
GenoGAM-class | GenoGAM class
GenoGAMDataSet | GenoGAMDataSet
GenoGAMDataSet-class | GenoGAMDataSet
GenoGAMDataSetList | GenoGAMDataSetList
GenoGAMDataSetList-class | GenoGAMDataSetList
GenoGAMFamily-class | GenoGAMFamily class
GenoGAMList | GenoGAMList class
GenoGAMList-class | GenoGAMList class
GenoGAMSettings | GenoGAMSettings
GenoGAMSettings-class | GenoGAMSettings
getChromosomes | GenoGAMDataSet
getChromosomes-method | GenoGAMDataSet
getChromosomes-method | GenoGAMDataSetList
getChunkSize | GenoGAMDataSet
getChunkSize-method | GenoGAMDataSet
getChunkSize-method | GenoGAMDataSetList
getChunkSize<- | GenoGAMDataSet
getChunkSize<--method | GenoGAMDataSet
getChunkSize<--method | GenoGAMDataSetList
getCoefs | GenoGAM class
getCoefs-method | GenoGAM class
getCoefs-method | GenoGAMList class
getCountMatrix-method | GenoGAMDataSet
getCountMatrix-method | GenoGAMDataSetList
getFamily | GenoGAM class
getFamily-method | GenoGAM class
getFamily-method | GenoGAMList class
getIndex | GenoGAMDataSet
getIndex-method | GenoGAMDataSet
getIndex-method | GenoGAMDataSetList
getKnots | GenoGAM class
getKnots-method | GenoGAM class
getKnots-method | GenoGAMList class
getOverhangSize | GenoGAMDataSet
getOverhangSize-method | GenoGAMDataSet
getOverhangSize-method | GenoGAMDataSetList
getOverhangSize<- | GenoGAMDataSet
getOverhangSize<--method | GenoGAMDataSet
getOverhangSize<--method | GenoGAMDataSetList
getParams | GenoGAM class
getParams-method | GenoGAM class
getParams-method | GenoGAMList class
getSettings | GenoGAM class
getSettings-method | GenoGAM class
getSettings-method | GenoGAMList class
getTileNumber | GenoGAMDataSet
getTileNumber-method | GenoGAMDataSet
getTileNumber-method | GenoGAMDataSetList
getTileNumber<- | GenoGAMDataSet
getTileNumber<--method | GenoGAMDataSet
getTileNumber<--method | GenoGAMDataSetList
getTileSize | GenoGAMDataSet
getTileSize-method | GenoGAMDataSet
getTileSize-method | GenoGAMDataSetList
getTileSize<- | GenoGAMDataSet
getTileSize<--method | GenoGAMDataSet
getTileSize<--method | GenoGAMDataSetList

## -- I --

IQR-method | Computing metrics
is.HDF5-method | GenoGAM class
is.HDF5-method | GenoGAMDataSet
is.HDF5-method | GenoGAMDataSetList
is.HDF5-method | GenoGAMList class

## -- L --

length-method | Coordinates class
length-method | GenoGAMDataSetList
length-method | GenoGAMList class

## -- M --

mad-method | Computing metrics
makeTestGenoGAM | Make an example /codeGenoGAM
makeTestGenoGAMDataSet | Make an example /codeGenoGAMDataSet
makeTestGenoGAMDataSetList | Make an example /codeGenoGAMDataSet
makeTestGenoGAMList | Make an example /codeGenoGAMList
mean-method | Computing metrics
median-method | Computing metrics

## -- N --

ncol-method | Coordinates class
nrow-method | Coordinates class

## -- P --

plotGenoGAM | The pot function for a GenoGAM object
pvalue-method | GenoGAM class
pvalue-method | GenoGAMList class

## -- R --

readData | Read Data function
rowRanges-method | GenoGAMDataSetList
rowRanges-method | GenoGAMList class

## -- S --

sd-method | Computing metrics
se | GenoGAM class
se-method | GenoGAM class
se-method | GenoGAMList class
seqlengths-method | GenoGAMDataSetList
seqlengths-method | GenoGAMList class
seqlevels-method | GenoGAMDataSetList
seqlevels-method | GenoGAMList class
seqlevelsInUse-method | GenoGAMDataSetList
seqlevelsInUse-method | GenoGAMList class
sizeFactors-method | GenoGAM class
sizeFactors-method | GenoGAMDataSet
sizeFactors-method | GenoGAMDataSetList
sizeFactors-method | GenoGAMList class
sizeFactors<--method | GenoGAMDataSet
sizeFactors<--method | GenoGAMDataSetList
start-method | Coordinates class
start<--method | Coordinates class
subset-method | Subset methods for GenoGAMDataSet
subset-method | Subset method for GenoGAMDataSetList
subset-method | Subset method for GenoGAMList
subsetByOverlaps-method | Subset methods for GenoGAMDataSet
subsetByOverlaps-method | Subset method for GenoGAMDataSetList
subsetByOverlaps-method | Subset method for GenoGAMList
Summary-method | Computing metrics
Summary-method | Computing metrics

## -- T --

tileSettings | GenoGAMDataSet
tileSettings-method | GenoGAMDataSet
tileSettings-method | GenoGAMDataSetList

## -- V --

var-method | Computing metrics

## -- W --

width-method | Coordinates class
writeToBEDFile | Write peaks to BED6+3/4 format

## -- misc --

[-method | GenoGAM class
[-method | Subset methods for GenoGAMDataSet
[-method | Subset method for GenoGAMDataSetList
[-method | Subset method for GenoGAMList