Man pages for GenoGAM
A GAM based framework for analysis of ChIP-Seq data

asDataFrameGenomicTiles to DataFrame
callPeaksCall peaks on a GenoGAM object
changeSettingsCheck data compliance with tile settings
checkSettingsCheck data compliance with tile settings
computeRegionSignificanceCompute significance for given regions
computeSignificanceCompute significance.
dataRangeThe /codeGRanges of the underlying data
designAccess the 'design' slot
filterDataA filter function for |codeGenoGAMDataSet
GenoGAMGenoGAM: A package providing a framework to analyse ChIP-Seq...
GenoGAM-classGenoGAM class
GenoGAMDataSetGenoGAMDataSet constructor.
GenoGAMDataSet-bracketsSubsetting by GRanges
GenoGAMDataSetToDataFrameGenoGAMDataSet to DataFrame
GenoGAMSettingsThe constructor function for GenoGAMSettings
GenoGAM-viewView the dataset
GenomicTilesGenomicTiles constructor.
GenomicTiles-bracketsProviding pseudo-list functionality
GenomicTiles-classGenomicTiles class
GenomicTiles-metricsComputing metrics
GenomicTiles-viewView the dataset
getChunkIndexCompute the index for chunks instead tiles
getCoordinatesAccessor to the /codecoordinates slot
getIndexAccessor to the 'index' slot
getIndexCoordinatesCompute the row coordinates for a given index
getTileTile extraction as a DataFrame
makeTestGenoGAMMake an example /codeGenoGAM
makeTestGenoGAMDataSetMake an example /codeGenoGAMDataSet
makeTestGenomicTilesMake an example /codeGenomicTile
plot.GenoGAMThe pot function for a GenoGAM object
qualityCheckA function to quality check the data
sizeFactorsAccess the 'sizeFactor' slot
subsetByOverlaps-GenoGAM-ANY-methodSubset by overlaps method for 'GenoGAM'
subsetByOverlaps-GenoGAMDataSet-GRanges-methodSubset by overlaps method for 'GenoGAMDataSet'
subsetByOverlaps-GenomicTiles-GRanges-methodSubset by overlaps method for 'GenomciTiles'
subset-GenoGAMDataSet-methodSubset method for 'GenoGAMDataSet'
subset-GenoGAM-methodSubset method for 'GenoGAM'
subset-GenomicTiles-methodSubset method for /codeGenomciTiles
tileSettingsReturn tile settings
tileSettings-elementsThe single entries of the tile settings
untileSet index to chunkIndex
writeToBEDFileWrite peaks to BED6+3/4 format
GenoGAM documentation built on May 2, 2018, 2:04 a.m.