Quality Control Tool for High-Throughput Sequencing Data


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Documentation for package ‘Rqc’ version 1.41.0

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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