A GAM based framework for analysis of ChIP-Seq data

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Documentation for package ‘GenoGAM’ version 2.8.0

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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