Analyze, manage and store genomic data

Documentation for package ‘Genominator’ version 1.30.0

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Genominator-package	Data backend for Genomic data
$-method	Class "ExpData"
addPrimingWeights	Adding priming weights to an AlignedRead object.
aggregateExpData	Collapse data into unique entries
applyMapped	Apply a function over mapped data.
chr1_yeast	Example datasets from Genominator
collapseExpData	Combine multiple data sets
computeCoverage	Compute effort-coverage values
computePrimingWeights	Compute weights to correct for random hexamer priming.
ExpData	Class "ExpData"
ExpData-class	Class "ExpData"
Genominator	Data backend for Genomic data
getColnames	Class "ExpData"
getDBConnection	Class "ExpData"
getDBFilename	Class "ExpData"
getIndexColumns	Class "ExpData"
getMode	Class "ExpData"
getRegion	Select a region from an ExpData object.
getSchema	Class "ExpData"
getTablename	Class "ExpData"
head-method	Class "ExpData"
importFromAlignedReads	Import aligned reads to database
importToExpData	Import data to database
initialize-method	Class "ExpData"
joinExpData	Merge ExpData objects
listTables	Class "ExpData"
makeGeneRepresentation	Compute a gene representation from annotation.
mergeWithAnnotation	Combine data with annotation
plot.genominator.coverage	Create coverage plot
plot.genominator.goodness.of.fit	Create goodness-of-fit quantile-quantile plot
regionGoodnessOfFit	Calculate goodness-of-fit statistics
regionGoodnessOfFit-method	Calculate goodness-of-fit statistics
regionGoodnessOfFit-methods	Calculate goodness-of-fit statistics
show-method	Class "ExpData"
splitByAnnotation	Split data into a list by annotation element.
summarizeByAnnotation	Summarize data based on genome annotation.
summarizeExpData	Summarize a data column
validAnnotation	Check for validity of a annotation object.
yeastAnno	Example datasets from Genominator
yeastAnno.sources	Example datasets from Genominator
[-method	Class "ExpData"