Quick Read Quality Control


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Documentation for package ‘qrqc’ version 1.24.0

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basePlot Plot Base Frequency or Proportion by Position
basePlot-method Plot Base Frequency or Proportion by Position
basePlot-methods Plot Base Frequency or Proportion by Position
calcKL Calculate the Kullback-Leibler Divergence Between the k-mer Distribution by Position and the k-mer Distribution Across All Positions.
calcKL-method Calculate the Kullback-Leibler Divergence Between the k-mer Distribution by Position and the k-mer Distribution Across All Positions.
FASTASummary-class 'FASTASummary' class representing the summaries of a FASTA file
FASTQSummary-class 'FASTQSummary' class representing the summaries of a FASTQ file
gcPlot Plot GC Content by Position
gcPlot-method Plot GC Content by Position
gcPlot-methods Plot GC Content by Position
geom_qlinerange Use Line Segments and Points to Plot Quality Statistics by Position in the Read
getBase Get a Data Frame of Base Frequency Data from a 'SequenceSummary' Object
getBase-method Get a Data Frame of Base Frequency Data from a 'SequenceSummary' Object
getBase-methods Get a Data Frame of Base Frequency Data from a 'SequenceSummary' Object
getBaseProp Get a Data Frame of Base Proportion Data from a 'SequenceSummary' object
getBaseProp-method Get a Data Frame of Base Proportion Data from a 'SequenceSummary' object
getBaseProp-methods Get a Data Frame of Base Proportion Data from a 'SequenceSummary' object
getGC Get a Data Frame of GC Content from a 'SequenceSummary' object
getGC-method Get a Data Frame of GC Content from a 'SequenceSummary' object
getGC-methods Get a Data Frame of GC Content from a 'SequenceSummary' object
getKmer Get a Data Frame of k-mer Frequency by Position from a 'SequenceSummary' Object
getKmer-method Get a Data Frame of k-mer Frequency by Position from a 'SequenceSummary' Object
getKmer-methods Get a Data Frame of k-mer Frequency by Position from a 'SequenceSummary' Object
getMCQual Get a Data Frame of Simulated Qualitied from a 'FASTQSummary' object
getMCQual-method Get a Data Frame of Simulated Qualitied from a 'FASTQSummary' object
getMCQual-methods Get a Data Frame of Simulated Qualitied from a 'FASTQSummary' object
getQual Get a Data Frame of Quality Data from a 'FASTQSummary' object
getQual-method Get a Data Frame of Quality Data from a 'FASTQSummary' object
getQual-methods Get a Data Frame of Quality Data from a 'FASTQSummary' object
getSeqlen Get a Data Frame of Sequence Lengths from a 'SequenceSummary' object
getSeqlen-method Get a Data Frame of Sequence Lengths from a 'SequenceSummary' object
getSeqlen-methods Get a Data Frame of Sequence Lengths from a 'SequenceSummary' object
kmerEntropyPlot Plot Entropy of k-mers by Position
kmerEntropyPlot-method Plot Entropy of k-mers by Position
kmerEntropyPlot-methods Plot Entropy of k-mers by Position
kmerKLPlot Plot K-L Divergence Components for a Subset of k-mers to Inspect for Contamination
kmerKLPlot-method Plot K-L Divergence Components for a Subset of k-mers to Inspect for Contamination
kmerKLPlot-methods Plot K-L Divergence Components for a Subset of k-mers to Inspect for Contamination
list2df Apply a function to items in list and combine into data frame
makeReport Make an HTML report from a FASTASummary of FASTQSummary object
makeReport-method 'FASTASummary' class representing the summaries of a FASTA file
makeReport-method 'FASTQSummary' class representing the summaries of a FASTQ file
makeReport-methods Make an HTML report from a FASTASummary of FASTQSummary object
plotBases Plot Bases by Position
plotBases-method 'SequenceSummary' class representing the summaries of a sequence file
plotBases-methods Plot Bases by Position
plotGC Plot per Base GC Content by Position
plotGC-method 'SequenceSummary' class representing the summaries of a sequence file
plotGC-methods Plot per Base GC Content by Position
plotQuals Plot a Base Quality Boxplot by Position
plotQuals-method 'FASTQSummary' class representing the summaries of a FASTQ file
plotQuals-methods Plot a Base Quality Boxplot by Position
plotSeqLengths Plot Histogram of Sequence Lengths
plotSeqLengths-method 'SequenceSummary' class representing the summaries of a sequence file
plotSeqLengths-methods Plot Histogram of Sequence Lengths
qualPlot Plot a Base Quality Boxplot by Position
qualPlot-method Plot a Base Quality Boxplot by Position
qualPlot-methods Plot a Base Quality Boxplot by Position
readSeqFile Read and Summarize a Sequence (FASTA or FASTQ) File
scale_color_dna Set the color scheme to 'biovizBase"s for DNA
scale_color_iupac Set the color scheme to 'biovizBase"s for IUPAC codes
seqlenPlot Plot a Histogram of Sequence Lengths
seqlenPlot-method Plot a Histogram of Sequence Lengths
seqlenPlot-methods Plot a Histogram of Sequence Lengths
SequenceSummary-class 'SequenceSummary' class representing the summaries of a sequence file