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

## Documentation for package ‘GenoGAM’ version 1.6.0

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

## Help Pages

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