A GAM based framework for analysis of ChIP-Seq data


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Documentation for package ‘GenoGAM’ version 1.0.3

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asDataFrame GenomicTiles to DataFrame
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
computeSignificance Compute significance.
computeSizeFactors computeSizeFactors
dataRange The /codeGRanges of the underlying data
dataRange-method The /codeGRanges of the underlying data
design-method Access the 'design' slot
design<--method Access the 'design' slot
GenoGAM GenoGAM: A package providing a framework to analyse ChIP-Seq data
genogam genogam
GenoGAM-class GenoGAM class
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 Accessor to 'fits' slot
getFits-method Accessor to 'fits' slot
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
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
[-method Providing pseudo-list functionality
[[-method Providing pseudo-list functionality