Reference

Object Classes
FastqcData()	The FastqcData Object Class
FastqcDataList()	The FastqcDataList Object Class
FastpData()	The FastpData Object Class
FastpDataList()	The FastpDataList Object Class
PwfCols-class PwfCols	The PwfCols class and associated methods
TheoreticalGC-class	The TheoreticalGC Object Class
Working With FastQC or Fastp Reports
getModule(<FastqcData>) getModule(<FastqcDataList>) getModule(<ANY>) getModule(<FastpData>) getModule(<FastpDataList>)	Retrieve a given module from a Fastqc* Object
getSummary(<.FastqcFile>) getSummary(<ANY>) getSummary(<FastqcData>) getSummary(<FastqcDataList>)	Get the summary information from Fastqc Files
plotReadTotals()	Draw a barplot of read totals
readTotals()	Get the read totals
plotSummary()	Plot the PASS/WARN/FAIL information
plotAdapterContent()	Draw an Adapter Content Plot
plotBaseQuals()	Plot the Base Qualities for each file
plotDupLevels()	Plot the combined Sequence_Duplication_Levels information
plotGcContent()	Plot the Per Sequence GC Content
plotInsertSize()	Plot Insert Size Distributions
plotKmers()	Plot Overrepresented Kmers
plotNContent()	Draw an N Content Plot
plotOverrep()	Plot a summary of Over-represented Sequences
summariseOverrep()	Summarise Overrepresented Sequences
plotFastqcPCA()	Draw a PCA plot for Fast QC modules
plotSeqContent()	Plot the per base content as a heatmap
plotSeqLengthDistn()	Plot the Sequence Length Distribution
plotSeqQuals()	Plot the Per Sequence Quality Scores
writeHtmlReport()	Write an HTML Summary Report
maxAdapterContent()	Get the maximum Adapter Content
fqName() `fqName<-`()	Return the Underlying Fastq File Names from Fastqc/Fastp Objects
fqcVersion(<FastqcData>) fqcVersion(<FastqcDataList>) fqcVersion(<ANY>)	Get the FASTQC version
Working With Other NGS Tools
importNgsLogs()	Import Various NGS-related log files
importSJ()	Import STAR Splice Junctions
plotAlignmentSummary()	Plot a summary of alignments
plotAssemblyStats()	Plot a summary of assembly logs
Utility Functions
estGcDistn()	Estimate a GC Content Distribution From Sequences
gcAvail()	List Genomes or Transcriptomes with Theoretical GC Content
getGC()	Get Theoretical GC content
getColours(<PwfCols>) setColours(<PwfCols>) setAlpha(<PwfCols>)	Work with objects of class PwfCols
overRep2Fasta()	Write fasta of Over-Represented sequences.
isCompressed()	Check to see if a file is compressed
path(<.FastqcFile>) path(<FastqcData>) path(<FastqcDataList>) path(<.FastpFile>) path(<FastpData>) path(<FastpDataList>)	Return the File Paths from an object
mData()	Extract Metadata for TheoreticalGC objects
Data Objects
gcTheoretical	Theoretical GC content
pwf	Colours for PASS/WARN/FAIL
All Methods
estGcDistn()	Estimate a GC Content Distribution From Sequences
`[`(<FastqcDataList>,<numeric>,<missing>) `[`(<FastqcDataList>,<character>,<missing>) `[`(<FastqcDataList>,<logical>,<missing>) `[`(<FastqcDataList>,<ANY>,<missing>) `[`(<FastpDataList>,<numeric>,<missing>) `[`(<FastpDataList>,<character>,<missing>) `[`(<FastpDataList>,<logical>,<missing>) `[`(<FastpDataList>,<ANY>,<missing>)	Extract Elements
fqName() `fqName<-`()	Return the Underlying Fastq File Names from Fastqc/Fastp Objects
fqcVersion(<FastqcData>) fqcVersion(<FastqcDataList>) fqcVersion(<ANY>)	Get the FASTQC version
gcAvail()	List Genomes or Transcriptomes with Theoretical GC Content
getColours(<PwfCols>) setColours(<PwfCols>) setAlpha(<PwfCols>)	Work with objects of class PwfCols
getGC()	Get Theoretical GC content
getModule(<FastqcData>) getModule(<FastqcDataList>) getModule(<ANY>) getModule(<FastpData>) getModule(<FastpDataList>)	Retrieve a given module from a Fastqc* Object
getSummary(<.FastqcFile>) getSummary(<ANY>) getSummary(<FastqcData>) getSummary(<FastqcDataList>)	Get the summary information from Fastqc Files
mData()	Extract Metadata for TheoreticalGC objects
overRep2Fasta()	Write fasta of Over-Represented sequences.
path(<.FastqcFile>) path(<FastqcData>) path(<FastqcDataList>) path(<.FastpFile>) path(<FastpData>) path(<FastpDataList>)	Return the File Paths from an object
plotAdapterContent()	Draw an Adapter Content Plot
plotBaseQuals()	Plot the Base Qualities for each file
plotDupLevels()	Plot the combined Sequence_Duplication_Levels information
plotFastqcPCA()	Draw a PCA plot for Fast QC modules
plotGcContent()	Plot the Per Sequence GC Content
plotInsertSize()	Plot Insert Size Distributions
plotKmers()	Plot Overrepresented Kmers
plotNContent()	Draw an N Content Plot
plotOverrep()	Plot a summary of Over-represented Sequences
plotReadTotals()	Draw a barplot of read totals
plotSeqContent()	Plot the per base content as a heatmap
plotSeqLengthDistn()	Plot the Sequence Length Distribution
plotSeqQuals()	Plot the Per Sequence Quality Scores
plotSummary()	Plot the PASS/WARN/FAIL information
summariseOverrep()	Summarise Overrepresented Sequences