Assessment of duplication rates in RNA-Seq datasets


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Documentation for package ‘dupRadar’ version 1.36.0

Help Pages

analyzeDuprates Read in a BAM file and count the tags falling on the features described in the GTF file
bamutilMarkDuplicates Mark duplicates using bamutil
cumulativeDuprateBarplot Barplot showing the cumulative read counts fraction
dm Duplication matrix of a good RNASeq experiment
dm.bad Duplication matrix of a failed RNASeq experiment
dupRadar dupRadar.
dupRadar_examples Example data containing precomputed matrices for two RNASeq experiments
duprateExpBoxplot Duplication rate ~ total reads per kilobase (RPK) boxplot
duprateExpDensPlot Duplication rate ~ total read count plot
duprateExpFit Duplication rate ~ total read count fit model
duprateExpIdentify Identify genes plotted by 'duprateExpPlot'
duprateExpPlot Duplication rate ~ total read count plot
expressionHist Draw histogram with the expression values
getBinDuplication Helper function used in 'duprateExpBoxplot'
getBinRpkMean Helper function used in 'duprateExpBoxplot'
getDupMatBin Helper function used in 'getBinDuplication' and 'getBinRpkMean'
getDupMatStats Report duplication stats on regions
getDynamicRange Dynamic range
getRpkBinReadCountFraction Helper function used in 'readcountExpressionBoxplot'
getRpkCumulativeReadCountFraction Helper function used in 'readcountExpressionBoxplot'
markDuplicates Program dispatchers to mark duplicated reads from a BAM file
picardMarkDuplicates Mark duplicates using Picard tools
readcountExpBoxplot Barplot of percentage of reads falling into expression bins