Quality Control Tool for High-Throughput Sequencing Data

[Up] [Top]

Documentation for package ‘Rqc’ version 1.2.0

Help Pages

Rqc-package Quality Control Tool for High-Throughput Sequencing Data
perCycleBasecall Frequency distribution of cycle-specific base call
perCycleQuality Frequency distribution of cycle-specific quality
perFileInformation File information
perReadQuality Frequency distribution of per read mean quality
perReadWidth Frequency distribution of read width
Rqc Quality Control Tool for High-Throughput Sequencing Data
rqc Main Rqc function
rqcCycleAverageQualityCalc Per cycle average quality calculation
rqcCycleAverageQualityPcaCalc PCA calculation of per cycle read average quality
rqcCycleAverageQualityPcaPlot Biplot of PCA of per cycle read average quality
rqcCycleAverageQualityPlot Per cycle average quality plot
rqcCycleBaseCallsCalc Per cycle base call calculation
rqcCycleBaseCallsLinePlot Per cycle base calls line plot
rqcCycleBaseCallsPlot Per cycle base calls plot
rqcCycleGCCalc Per cycle percentual GC.
rqcCycleGCPlot Per cycle percentual GC plot
rqcCycleQualityBoxCalc Per cycle quality percentiles calculation for boxplot
rqcCycleQualityBoxPlot Per cycle quality box plot
rqcCycleQualityCalc Per cycle quality calculation
rqcCycleQualityPlot Per cycle quality plot
rqcQA Quality Assessment Rqc function
rqcReadQualityBoxCalc Per read mean quality percentiles calculation for boxplot
rqcReadQualityBoxPlot Per read mean quality box plot
rqcReadQualityCalc Per read quality calculation
rqcReadQualityPlot Per read quality plot
rqcReadWidthCalc Per read width calculation
rqcReadWidthPlot Per read width plot
rqcReport Quality Control HTML Report
RqcResultSet Quality control data
RqcResultSet-class Quality control data
stats4trim Minimun read mean quality and maximum percentage loss of reads estimations for trimming step.