# Load FastqQC reports and other NGS related files

## Documentation for package ‘ngsReports’ version 2.0.0

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

## Help Pages

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