Function reference • dupRadar

All functions
`analyzeDuprates()`	Read in a BAM file and count the tags falling on the features described in the GTF file
`bamutilMarkDuplicates()`	Mark duplicates using bamutil
`cumulativeDuprateBarplot()`	Barplot showing the cumulative read counts fraction
`dupRadar_examples`	Duplication matrix of a good RNASeq experiment
`dupRadar_examples`	Duplication matrix of a failed RNASeq experiment
`dupRadar`	dupRadar.
`dupRadar_examples`	Example data containing precomputed matrices for two RNASeq experiments
`duprateExpBoxplot()`	Duplication rate ~ total reads per kilobase (RPK) boxplot
`duprateExpDensPlot()`	Duplication rate ~ total read count plot
`duprateExpFit()`	Duplication rate ~ total read count fit model
`duprateExpIdentify()`	Identify genes plotted by `duprateExpPlot`
`duprateExpPlot()`	Duplication rate ~ total read count plot
`expressionHist()`	Draw histogram with the expression values
`getBinDuplication()`	Helper function used in `duprateExpBoxplot`
`getBinRpkMean()`	Helper function used in `duprateExpBoxplot`
`getDupMatBin()`	Helper function used in `getBinDuplication` and `getBinRpkMean`
`getDupMatStats()`	Report duplication stats on regions
`getDynamicRange()`	Dynamic range
`getRpkBinReadCountFraction()`	Helper function used in `readcountExpressionBoxplot`
`getRpkCumulativeReadCountFraction()`	Helper function used in `readcountExpressionBoxplot`
`markDuplicates()`	Program dispatchers to mark duplicated reads from a BAM file
`picardMarkDuplicates()`	Mark duplicates using Picard tools
`readcountExpBoxplot()`	Barplot of percentage of reads falling into expression bins

Reference

All functions