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 |
asCoordinates | IRanges to Coordinates |
assay-method | GenoGAM class |
assay-method | GenoGAMDataSetList |
assay-method | GenoGAMList class |
assays-method | GenoGAMDataSetList |
assays-method | GenoGAMList class |
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 |
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 |
end-method | Coordinates class |
end<--method | Coordinates class |
fits | GenoGAM class |
fits-method | GenoGAM class |
fits-method | GenoGAMList class |
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 |
IQR-method | Computing metrics |
is.HDF5-method | GenoGAM class |
is.HDF5-method | GenoGAMDataSet |
is.HDF5-method | GenoGAMDataSetList |
is.HDF5-method | GenoGAMList class |
length-method | Coordinates class |
length-method | GenoGAMDataSetList |
length-method | GenoGAMList class |
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 |
ncol-method | Coordinates class |
nrow-method | Coordinates class |
plotGenoGAM | The pot function for a GenoGAM object |
pvalue-method | GenoGAM class |
pvalue-method | GenoGAMList class |
readData | Read Data function |
rowRanges-method | GenoGAMDataSetList |
rowRanges-method | GenoGAMList class |
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 |
tileSettings | GenoGAMDataSet |
tileSettings-method | GenoGAMDataSet |
tileSettings-method | GenoGAMDataSetList |
var-method | Computing metrics |
width-method | Coordinates class |
writeToBEDFile | Write peaks to BED6+3/4 format |
[-method | GenoGAM class |
[-method | Subset methods for GenoGAMDataSet |
[-method | Subset method for GenoGAMDataSetList |
[-method | Subset method for GenoGAMList |