# Quality Control Tool for High-Throughput Sequencing Data

## Documentation for package ‘Rqc’ version 1.40.0

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

## Help Pages

Rqc-package | Quality Control Tool for High-Throughput Sequencing Data
checkpoint | Save time storing longer analysis step on disk
detectFileFormat | Detect file format
fromRRDNA | Revert codified DNA sequences to original DNA sequences.
matdist | Distance matrix of the similarity between the DNA sequences.
perCycleBasecall | Class RqcResultSet
perCycleBasecall-method | Class RqcResultSet
perCycleQuality | Class RqcResultSet
perCycleQuality-method | Class RqcResultSet
perFileInformation | Class RqcResultSet
perFileInformation-method | Class RqcResultSet
perFileTopReads | Class RqcResultSet
perFileTopReads-method | Class RqcResultSet
perReadFrequency | Class RqcResultSet
perReadFrequency-method | Class RqcResultSet
perReadQuality | Class RqcResultSet
perReadQuality-method | Class RqcResultSet
perReadWidth | Class RqcResultSet
perReadWidth-method | Class RqcResultSet
Rqc | Quality Control Tool for High-Throughput Sequencing Data
rqc | Main Rqc function
rqcCycleAverageQualityCalc | Per cycle average quality by files
rqcCycleAverageQualityPcaCalc | Biplot of PCA of per cycle read average quality
rqcCycleAverageQualityPcaPlot | Biplot of PCA of per cycle read average quality
rqcCycleAverageQualityPlot | Per cycle average quality by files
rqcCycleBaseCallsCalc | Per cycle base calls plot
rqcCycleBaseCallsLinePlot | Per cycle base calls plot
rqcCycleBaseCallsPlot | Per cycle base calls plot
rqcCycleGCCalc | Per cycle percentual GC plot
rqcCycleGCPlot | Per cycle percentual GC plot
rqcCycleQualityBoxCalc | Per cycle quality box plot
rqcCycleQualityBoxPlot | Per cycle quality box plot
rqcCycleQualityCalc | Per cycle quality plot
rqcCycleQualityPlot | Per cycle quality plot
rqcFileHeatmap | Heatmap of distance matrix of top over-represented reads
rqcGroupCycleAverageQualityCalc | Per group average quality across cycles
rqcGroupCycleAverageQualityPlot | Per group average quality across cycles
rqcQA | Quality Assessment Rqc function
rqcQA-method | Quality Assessment Rqc function
rqcReadFrequencyCalc | Read frequency plot
rqcReadFrequencyPlot | Read frequency plot
rqcReadQualityBoxCalc | Per read mean quality box plot
rqcReadQualityBoxPlot | Per read mean quality box plot
rqcReadQualityCalc | Per read quality plot
rqcReadQualityPlot | Per read quality plot
rqcReadWidthCalc | Per read width plot
rqcReadWidthPlot | Per read width plot
rqcReport | Quality Control HTML Report
RqcResultSet-class | Class RqcResultSet
rqcShinyReport | Interactive Quality Control Report
stats4trim | Minimun read mean quality and maximum percentage loss of reads estimations for trimming step.
subsetByGroup | Subset RqcResultSet object by group name.
subsetByPair | Subset RqcResultSet object by pair files.
toRRDNA | Title: Convert DNA sequences to Reduced Representation format