Analyze, manage and store genomic data


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Documentation for package ‘Genominator’ version 1.10.0

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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"