Analyze genomic data

Documentation for package ‘Genominator’ version 1.0.3

Genominator-package	Data backend for Genomic data
$,ExpData-method	Class "ExpData"
aggregateExpData	Collapse data into unique entries
applyMapped	Apply a function over mapped data.
collapseExpData	Combine multiple data sets
computeCoverage	Compute effort-coverage values
ExpData	Class "ExpData"
ExpData-class	Class "ExpData"
Genominator	Data backend for Genomic data
getColnames	Class "ExpData"
getDB	Class "ExpData"
getDBName	Class "ExpData"
getIndexColumns	Class "ExpData"
getMode	Class "ExpData"
getRegion	Select a region from an \code{ExpData} object.
getSchema	Class "ExpData"
getTablename	Class "ExpData"
head,ExpData-method	Class "ExpData"
importFromAlignedReads	Import aligned reads to database
importToExpData	Import data to database
initialize,ExpData-method	Class "ExpData"
joinExpData	Merge ExpData objects
listTables	Class "ExpData"
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,data.frame-method	Calculate goodness-of-fit statistics
regionGoodnessOfFit,ExpData-method	Calculate goodness-of-fit statistics
regionGoodnessOfFit-methods	Calculate goodness-of-fit statistics
show,ExpData-method	Class "ExpData"
splitByAnnotation	Split data into a list by annotation element.
summarizeByAnnotation	Summarize data based on genome annotation.
summarizeExpData	Summarize a data column
[,ExpData-method	Class "ExpData"