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

## Documentation for package ‘R453Plus1Toolbox’ version 1.2.2

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

A B C D E F G H L M N P R S T misc

## -- A --

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
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 --

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
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"
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

## -- 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.

## -- G --

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
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 --

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

## -- 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"

## -- N --

names-method | Class "AnnotatedVariants"
names-method | Class "Breakpoints"
names<--method | Class "AnnotatedVariants"
names<--method | Class "Breakpoints"

## -- 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

## -- R --

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
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
setVariantFilter | Filters output of variant information
setVariantFilter-method | Class to contain Amplicon Variant Analyzer Output
setVariantFilter-method | Class to Contain GS Reference Mapper Output

## -- T --

transcriptdf | Ensembl transcript information for variant plotting

## -- misc --

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