Quality Control Tool for High-Throughput Sequencing Data

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Documentation for package ‘Rqc’ version 1.41.0

• 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