# Quality of RNA-seq Tool

## Documentation for package ‘QoRTs’ version 1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

build.plotter | Generating plotters
build.plotter.advanced | Generating plotters
build.plotter.basic | Generating plotters
build.plotter.colorByGroup | Generating plotters
build.plotter.colorByLane | Generating plotters
build.plotter.colorBySample | Generating plotters
build.plotter.colorByX | Generating plotters
build.plotter.highlightSample | Generating plotters
build.plotter.highlightSample.colorByLane | Generating plotters
completeAndCheckDecoder | Reading QC results data
get.size.factors | Get summary data tables
get.summary.table | Get summary data tables
makeMultiPlot | Generating summary multi-plots
makeMultiPlot.all | Generating all default plots
makeMultiPlot.basic | Generating summary multi-plots
makeMultiPlot.colorByGroup | Generating summary multi-plots
makeMultiPlot.colorByLane | Generating summary multi-plots
makeMultiPlot.colorBySample | Generating summary multi-plots
makeMultiPlot.highlightSample | Generating summary multi-plots
makeMultiPlot.highlightSample.all | Generating sample highlight multi-plots
makeMultiPlot.highlightSample.colorByLane | Generating summary multi-plots
makeMultiPlot.highlightSample.colorByLane.all | Generating sample highlight multi-plots
makeMultiPlot.withPlotter | Generating summary multi-plots
makePlot.biotype.rates | Plot Biotype rates
makePlot.chrom.type.rates | Chromosome type rate plot
makePlot.cigarLength.distribution | Plot the length distribution of a given cigar operation
makePlot.cigarOp.byCycle | Plot Cigar Operator Rate
makePlot.clipping | Plot Alignment Clipping
makePlot.dropped.rates | Read Drop Plot
makePlot.gc | Plot GC content
makePlot.gene.assignment.rates | Gene assignment rate plot
makePlot.gene.cdf | Plot the cumulative gene diversity curve
makePlot.genebody | Plot Gene-Body coverage distribution
makePlot.genebody.coverage | Plot Gene-Body coverage distribution
makePlot.genebody.coverage.lowExpress | Plot Gene-Body coverage distribution
makePlot.genebody.coverage.UMQuartile | Plot Gene-Body coverage distribution
makePlot.insert.size | Plot Insert Size Distribution.
makePlot.legend.box | Plot legend
makePlot.legend.over | Plot legend
makePlot.mapping.rates | Plot mapping rates
makePlot.minus.clipping.NVC | Nucleotide-rate by read cycle plot
makePlot.missingness.rate | Plot N-Rate by read cycle
makePlot.norm.factors | Plot Alignment Clipping
makePlot.norm.factors.vs.TC | Plot Alignment Clipping
makePlot.NVC | Nucleotide-rate by read cycle plot
makePlot.NVC.clip.matchByClipPosition | Plot clipped nucleotide rates, aligned by the distance from the point of clipping.
makePlot.NVC.lead.clip | Clipped sequence nucleotide-by-position plot
makePlot.NVC.lead.clip.matchByClipPosition | Plot clipped nucleotide rates, aligned by the distance from the point of clipping.
makePlot.NVC.tail.clip | Clipped sequence nucleotide-by-position plot
makePlot.NVC.tail.clip.matchByClipPosition | Plot clipped nucleotide rates, aligned by the distance from the point of clipping.
makePlot.onTarget.counts | On-Target Rates
makePlot.onTarget.rates | On-Target Rates
makePlot.overlap | Overlap Mismatch Rates
makePlot.overlap.coverage | Overlap Mismatch Rates
makePlot.overlapMismatch.byBase | Overlap Mismatch Rates
makePlot.overlapMismatch.byBase.atScore | Overlap Mismatch Rates
makePlot.overlapMismatch.byCycle | Overlap Mismatch Rates
makePlot.overlapMismatch.byQual.min | Overlap Mismatch Rates
makePlot.overlapMismatch.byQual.read | Overlap Mismatch Rates
makePlot.overlapMismatch.perRead | Overlap Mismatch Rates
makePlot.overlapMismatch.size | Overlap Mismatch Rates
makePlot.qual.pair | Plot quality score by read cycle
makePlot.raw.NVC | Nucleotide-rate by read cycle plot
makePlot.readLengthDist | Plot the distribution of read lengths.
makePlot.reference | Plot Reference Mismatch Rates
makePlot.referenceMismatch | Plot Reference Mismatch Rates
makePlot.referenceMismatch.byBase | Plot Reference Mismatch Rates
makePlot.referenceMismatch.byBase.atScore | Plot Reference Mismatch Rates
makePlot.referenceMismatch.byCycle | Plot Reference Mismatch Rates
makePlot.referenceMismatch.byScore | Plot Reference Mismatch Rates
makePlot.referenceMismatch.perRead | Plot Reference Mismatch Rates
makePlot.runTimePerformance | Chromosome type rate plot
makePlot.splice.junction.event | Plot Splice Junction Event Rates
makePlot.splice.junction.event.counts | Plot Splice Junction Event Rates
makePlot.splice.junction.event.proportions | Plot Splice Junction Event Rates
makePlot.splice.junction.event.proportionsByType | Plot Splice Junction Event Rates
makePlot.splice.junction.event.ratesPerRead | Plot Splice Junction Event Rates
makePlot.splice.junction.loci.counts | Splice Junction Loci Count Plot
makePlot.strandedness.test | Strandedness Test Plot
makePlot.targetDistribution | On-Target Rates
plotter | Generating plotters
QoRTs.default.plotting.params | Generating plotters
read.qc.results.data | Reading QC results data