# A package for importing and analyzing data from Roche's Genome Sequencer System

## Documentation for package ‘R453Plus1Toolbox’ version 1.38.0

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

## Help Pages

A B C D E F G H K L M N P Q R S V W misc

## -- A --

addRead | Class '"SFFContainer"'
addRead-method | Class '"SFFContainer"'
alignedReadsC1 | Class "Breakpoints"
alignedReadsC1-method | Class "Breakpoints"
alignedReadsC1<- | Class "Breakpoints"
alignedReadsC1<--method | Class "Breakpoints"
alignedReadsC2 | Class "Breakpoints"
alignedReadsC2-method | Class "Breakpoints"
alignedReadsC2<- | Class "Breakpoints"
alignedReadsC2<--method | Class "Breakpoints"
alignShortReads | Exact alignment of DNA sequences against a reference
alignShortReads-method | Class to contain Amplicon Variant Analyzer Output
alignShortReads-method | Exact alignment of DNA sequences against a reference
annotatedVariants | Class "AnnotatedVariants"
AnnotatedVariants-class | Class "AnnotatedVariants"
annotatedVariants-method | Class "AnnotatedVariants"
annotatedVariants<--method | Class "AnnotatedVariants"
annotateVariants | Adds genomic information to variants
annotateVariants-method | Class to contain Amplicon Variant Analyzer Output
annotateVariants-method | Class to Contain GS Reference Mapper Output
annotateVariants-method | Adds genomic information to variants
assayDataAmp | Access the amplicon data of an AVASet.
assayDataAmp-method | Class to contain Amplicon Variant Analyzer Output
assayDataAmp<- | Class to contain Amplicon Variant Analyzer Output
assayDataAmp<--method | Class to contain Amplicon Variant Analyzer Output
ava2vcf | Convert an AVASet object into a VCF object
ava2vcf-method | Convert an AVASet object into a VCF object
AVASet | Creating an AVASet
AVASet-class | Class to contain Amplicon Variant Analyzer Output
AVASet-method | Creating an AVASet
avaSetExample | Amplicon Variant Analyzer data import
avaSetFiltered | Amplicon Variant Analyzer data import
avaSetFiltered_annot | AVASet variant annotations

## -- B --

baseFrequency | Absolute And Relative Frequency Of The Four Bases.
baseFrequency-method | Absolute And Relative Frequency Of The Four Bases.
baseQualityHist | Plot A Histogram Of The Base Qualities.
baseQualityHist-method | Plot A Histogram Of The Base Qualities.
baseQualityStats | Statistics Of Base Quality
baseQualityStats-method | Statistics Of Base Quality
breakpoints | Putative breakpoints of chimeric reads
Breakpoints-class | Class "Breakpoints"

## -- C --

calculateTiTv | Calculate transition transversion ratio
calculateTiTv-method | Calculate transition transversion ratio
captureArray | Custom capture array design
clipAdapterLeft | Class '"SFFContainer"'
clipAdapterLeft-method | Class '"SFFContainer"'
clipAdapterLeft-method | Class '"SFFRead"'
clipAdapterLeft<- | Class '"SFFContainer"'
clipAdapterLeft<--method | Class '"SFFContainer"'
clipAdapterLeft<--method | Class '"SFFRead"'
clipAdapterRight | Class '"SFFContainer"'
clipAdapterRight-method | Class '"SFFContainer"'
clipAdapterRight-method | Class '"SFFRead"'
clipAdapterRight<- | Class '"SFFContainer"'
clipAdapterRight<--method | Class '"SFFContainer"'
clipAdapterRight<--method | Class '"SFFRead"'
clipQualityLeft | Class '"SFFContainer"'
clipQualityLeft-method | Class '"SFFContainer"'
clipQualityLeft-method | Class '"SFFRead"'
clipQualityLeft<- | Class '"SFFContainer"'
clipQualityLeft<--method | Class '"SFFContainer"'
clipQualityLeft<--method | Class '"SFFRead"'
clipQualityRight | Class '"SFFContainer"'
clipQualityRight-method | Class '"SFFContainer"'
clipQualityRight-method | Class '"SFFRead"'
clipQualityRight<- | Class '"SFFContainer"'
clipQualityRight<--method | Class '"SFFContainer"'
clipQualityRight<--method | Class '"SFFRead"'
commonAlignC1 | Class "Breakpoints"
commonAlignC1-method | Class "Breakpoints"
commonAlignC1<- | Class "Breakpoints"
commonAlignC1<--method | Class "Breakpoints"
commonAlignC2 | Class "Breakpoints"
commonAlignC2-method | Class "Breakpoints"
commonAlignC2<- | Class "Breakpoints"
commonAlignC2<--method | Class "Breakpoints"
commonBpsC1 | Class "Breakpoints"
commonBpsC1-method | Class "Breakpoints"
commonBpsC1<- | Class "Breakpoints"
commonBpsC1<--method | Class "Breakpoints"
commonBpsC2 | Class "Breakpoints"
commonBpsC2-method | Class "Breakpoints"
commonBpsC2<- | Class "Breakpoints"
commonBpsC2<--method | Class "Breakpoints"
complexity.dust | Sequence Complexity Using The DUST Algorithm
complexity.dust-method | Sequence Complexity Using The DUST Algorithm
complexity.entropy | Sequence Complexity Using The Shannon-Wiener Algorithm
complexity.entropy-method | Sequence Complexity Using The Shannon-Wiener Algorithm
convertCigar | Basic functions for CIGAR strings
coverageOnTarget | Computes the coverage restricted to the target region.
coverageOnTarget-method | Computes the coverage restricted to the target region.

## -- D --

demultiplexReads | Performs MID/Multiplex filtering
demultiplexReads-method | Performs MID/Multiplex filtering
detectBreakpoints | Clustering and consensus breakpoint detection for chimeric reads
detectBreakpoints-method | Clustering and consensus breakpoint detection for chimeric reads
dinucleotideOddsRatio | Dinucleotide Odds Ratio
dinucleotideOddsRatio-method | Dinucleotide Odds Ratio

## -- E --

extendedCIGARToList | Basic functions for CIGAR strings

## -- F --

fDataAmp | Access the amplicon data of an AVASet.
fDataAmp-method | Class to contain Amplicon Variant Analyzer Output
featureDataAmp | Access the amplicon data of an AVASet
featureDataAmp-method | Class to contain Amplicon Variant Analyzer Output
featureDataAmp<- | Class to contain Amplicon Variant Analyzer Output
featureDataAmp<--method | Class to contain Amplicon Variant Analyzer Output
filterChimericReads | Extract chimeric reads and apply filtering steps to remove artificial chimeric reads.
filterChimericReads-method | Extract chimeric reads and apply filtering steps to remove artificial chimeric reads.
flowChars | Class '"SFFContainer"'
flowChars-method | Class '"SFFContainer"'
flowChars-method | Class '"SFFRead"'
flowChars<- | Class '"SFFContainer"'
flowChars<--method | Class '"SFFContainer"'
flowChars<--method | Class '"SFFRead"'
flowgram | Class '"SFFRead"'
flowgram-method | Class '"SFFRead"'
flowgram<- | Class '"SFFRead"'
flowgram<--method | Class '"SFFRead"'
flowgramBarplot | Create A Barplot Of The Flow Intensities
flowgramBarplot-method | Create A Barplot Of The Flow Intensities
flowgramFormat | Class '"SFFContainer"'
flowgramFormat-method | Class '"SFFContainer"'
flowgramFormat-method | Class '"SFFRead"'
flowgramFormat<- | Class '"SFFContainer"'
flowgramFormat<--method | Class '"SFFContainer"'
flowgramFormat<--method | Class '"SFFRead"'
flowgrams | Class '"SFFContainer"'
flowgrams-method | Class '"SFFContainer"'
flowgrams<- | Class '"SFFContainer"'
flowgrams<--method | Class '"SFFContainer"'
flowIndexes | Class '"SFFContainer"'
flowIndexes-method | Class '"SFFContainer"'
flowIndexes-method | Class '"SFFRead"'
flowIndexes<- | Class '"SFFContainer"'
flowIndexes<--method | Class '"SFFContainer"'
flowIndexes<--method | Class '"SFFRead"'

## -- G --

gcContent | Calculate The Overall GC-Content
gcContent-method | Calculate The Overall GC-Content
gcContentHist | GC-Content Histogram
gcContentHist-method | GC-Content Histogram
gcPerPosition | GC-Content Per Position
gcPerPosition-method | GC-Content Per Position
genomeSequencerMIDs | Retrieve GS multiplex sequences
genomeSequencerMIDs-method | Retrieve GS multiplex sequences
getAlignedReads | Import reads from an Amplicon Variant Analyzer project
getAlignedReads-method | Import reads from an Amplicon Variant Analyzer project
getAminoAbbr | Get amino acid abbreviations
getRead | Class '"SFFContainer"'
getRead-method | Class '"SFFContainer"'
getReadStatus | Class to Contain GS Reference Mapper Output
getReadStatus-method | Class to Contain GS Reference Mapper Output
getVariantPercentages | Variant coverage
getVariantPercentages-method | Class to contain Amplicon Variant Analyzer Output
getVariantPercentages-method | Class to Contain GS Reference Mapper Output

## -- H --

homopolymerHist | Create A Histogram Of The Homopolymer Stretches
homopolymerHist-method | Create A Histogram Of The Homopolymer Stretches
htmlReport | HTML-Report Builder for the AVASet and MapperSet
htmlReport-method | Class to contain Amplicon Variant Analyzer Output
htmlReport-method | Class to Contain GS Reference Mapper Output

## -- K --

keySequence | Class '"SFFContainer"'
keySequence-method | Class '"SFFContainer"'
keySequence-method | Class '"SFFRead"'
keySequence<- | Class '"SFFContainer"'
keySequence<--method | Class '"SFFContainer"'
keySequence<--method | Class '"SFFRead"'

## -- L --

length-method | Class "Breakpoints"
listToExtendedCIGAR | Basic functions for CIGAR strings

## -- M --

MapperSet | Creating a MapperSet
MapperSet-class | Class to Contain GS Reference Mapper Output
MapperSet-method | Creating a MapperSet
mapperSetExample | GS Reference Mapper data import
mergeBreakpoints | Identify and merge related breakpoints caused by the same variant.
mergeBreakpoints-method | Class "Breakpoints"
mutationInfo | Example data for 'plotVariants'

## -- N --

name | Class '"SFFContainer"'
name-method | Class '"SFFContainer"'
name-method | Class '"SFFRead"'
name<- | Class '"SFFContainer"'
name<--method | Class '"SFFContainer"'
name<--method | Class '"SFFRead"'
names-method | Class "AnnotatedVariants"
names-method | Class "Breakpoints"
names<--method | Class "AnnotatedVariants"
names<--method | Class "Breakpoints"
nucleotideCharts | Nucleotide Charts
nucleotideCharts-method | Nucleotide Charts

## -- P --

plotAmpliconCoverage | Creates a plot visualizing the number of reads per amplicon
plotAmpliconCoverage-method | Creates a plot visualizing the number of reads per amplicon
plotChimericReads | Plots chimeric reads
plotChimericReads-method | Class "Breakpoints"
plotVariants | Plots variant positions
plotVariants-method | Plots variant positions
plotVariationFrequency | Create an AVA style variation frequency plot
plotVariationFrequency-method | Create an AVA style variation frequency plot
positionQualityBoxplot | Boxplot Of The Quality For Each Position
positionQualityBoxplot-method | Boxplot Of The Quality For Each Position

## -- Q --

quality-method | Class '"SFFRead"'
quality<- | Class '"SFFRead"'
quality<--method | Class '"SFFRead"'
qualityReportSFF | Function To Create A Quality Report In PDF Format

## -- R --

read | Class '"SFFRead"'
read-method | Class '"SFFRead"'
read<- | Class '"SFFRead"'
read<--method | Class '"SFFRead"'
readLengthHist | Histogram Of The Read Lengths
readLengthHist-method | Histogram Of The Read Lengths
readLengthStats | Statistics For The Read Lengths
readLengthStats-method | Statistics For The Read Lengths
reads | Class '"SFFContainer"'
reads-method | Class '"SFFContainer"'
reads<- | Class '"SFFContainer"'
reads<--method | Class '"SFFContainer"'
readSFF | Function To Read In Roche's .sff Files
readsOnTarget | Check for each read whether it aligns within the given region.
readsOnTarget-method | Check for each read whether it aligns within the given region.
referenceSequences | Access the reference sequences of an AVASet
referenceSequences-method | Class to contain Amplicon Variant Analyzer Output
referenceSequences<- | Class to contain Amplicon Variant Analyzer Output
referenceSequences<--method | Class to contain Amplicon Variant Analyzer Output
regions | Example data for 'plotVariants'
removeLinker | Remove linker sequences located at the start of short reads
removeLinker-method | Remove linker sequences located at the start of short reads

## -- S --

seqsC1 | Class "Breakpoints"
seqsC1-method | Class "Breakpoints"
seqsC1<- | Class "Breakpoints"
seqsC1<--method | Class "Breakpoints"
seqsC2 | Class "Breakpoints"
seqsC2-method | Class "Breakpoints"
seqsC2<- | Class "Breakpoints"
seqsC2<--method | Class "Breakpoints"
sequenceCaptureLinkers | Retrieve NimbleGen's sequence capture linkers
sequenceCaptureLinkers-method | Retrieve NimbleGen's sequence capture linkers
sequenceQualityHist | A Histogram Of The Sequence Qualities
sequenceQualityHist-method | A Histogram Of The Sequence Qualities
setVariantFilter | Filters output of variant information
setVariantFilter-method | Class to contain Amplicon Variant Analyzer Output
setVariantFilter-method | Class to Contain GS Reference Mapper Output
sff2fastq | Write A SFFContainer Object To A FASTQ File
sff2fastq-method | Write A SFFContainer Object To A FASTQ File
SFFContainer | Class '"SFFContainer"'
SFFContainer-class | Class '"SFFContainer"'
SFFRead | Class '"SFFRead"'
SFFRead-class | Class '"SFFRead"'

## -- V --

variants | Example data for 'plotVariants'

## -- W --

writeSFF | Function To Write Files In Roche's .sff Format

## -- misc --

[-method | Class to contain Amplicon Variant Analyzer Output
[-method | Class "Breakpoints"
[-method | Class '"SFFContainer"'