# Quick Read Quality Control

## Documentation for package ‘qrqc’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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