Package: R453Plus1Toolbox 1.55.0

Hans-Ulrich Klein

R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.

Authors:Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert

# Install 'R453Plus1Toolbox' in R:

install.packages('R453Plus1Toolbox', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

avaSetExample - Amplicon Variant Analyzer data import
avaSetFiltered - Amplicon Variant Analyzer data import
avaSetFiltered_annot - AVASet variant annotations
breakpoints - Putative breakpoints of chimeric reads
captureArray - Custom capture array design
mapperSetExample - GS Reference Mapper data import
mutationInfo - Example data for 'plotVariants'
regions - Example data for 'plotVariants'
variants - Example data for 'plotVariants'

On BioConductor:R453Plus1Toolbox-1.55.0(bioc 3.20)R453Plus1Toolbox-1.54.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

100 exports 0.91 score 108 dependencies 1 mentions

Last updated 2 months agofrom:aaba7c4330

Exports:addRead alignedReadsC1 alignedReadsC1<-alignedReadsC2 alignedReadsC2<-alignShortReads annotatedVariants annotateVariants assayDataAmp assayDataAmp<-ava2vcf AVASet baseFrequency baseQualityHist baseQualityStats calculateTiTv clipAdapterLeft clipAdapterLeft<-clipAdapterRight clipAdapterRight<-clipQualityLeft clipQualityLeft<-clipQualityRight clipQualityRight<-commonAlignC1 commonAlignC1<-commonAlignC2 commonAlignC2<-commonBpsC1 commonBpsC1<-commonBpsC2 commonBpsC2<-complexity.dust complexity.entropy coverageOnTarget demultiplexReads detectBreakpoints dinucleotideOddsRatio extendedCIGARToList fDataAmp featureDataAmp featureDataAmp<-filterChimericReads flowChars flowChars<-flowgram flowgram<-flowgramBarplot flowgramFormat flowgramFormat<-flowgrams flowgrams<-flowIndexes flowIndexes<-gcContent gcContentHist gcPerPosition genomeSequencerMIDs getAlignedReads getRead getReadStatus getVariantPercentages homopolymerHist htmlReport keySequence keySequence<-listToExtendedCIGAR MapperSet mergeBreakpoints name name<-nucleotideCharts plotAmpliconCoverage plotChimericReads plotVariants plotVariationFrequency positionQualityBoxplot quality quality<-qualityReportSFF read read<-readLengthHist readLengthStats reads reads<-readSFF readsOnTarget referenceSequences referenceSequences<-removeLinker seqsC1 seqsC1<-seqsC2 seqsC2<-sequenceCaptureLinkers sequenceQualityHist setVariantFilter sff2fastq writeSFF

Dependencies:abind AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray deldir digest dplyr fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 hwriter interp IRanges jpeg jsonlite KEGGREST lambda.r lattice latticeExtra lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png prettyunits progress purrr pwalign R2HTML R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors ShortRead snow SparseArray stringi stringr SummarizedExperiment sys TeachingDemos tibble tidyr tidyselect UCSC.utils utf8 VariantAnnotation vctrs withr XML xml2 xtable XVector yaml zlibbioc

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

Rendered fromvignette.Rnwusingutils::Sweaveon Jun 20 2024.

Last update: 2018-01-22
Started: 2013-10-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Exact alignment of DNA sequences against a reference	alignShortReads alignShortReads,AVASet,BSgenome,character,logical-method alignShortReads,AVASet,BSgenome,character,missing-method alignShortReads,AVASet,BSgenome,missing,logical-method alignShortReads,AVASet,BSgenome,missing,missing-method alignShortReads,DNAStringSet,BSgenome,character,logical-method alignShortReads,DNAStringSet,BSgenome,character,missing-method alignShortReads,DNAStringSet,BSgenome,missing,logical-method alignShortReads,DNAStringSet,BSgenome,missing,missing-method
Class "AnnotatedVariants"	annotatedVariants annotatedVariants,AnnotatedVariants-method AnnotatedVariants-class annotatedVariants<-,AnnotatedVariants,list-method names,AnnotatedVariants-method names<-,AnnotatedVariants,character-method
Adds genomic information to variants	annotateVariants annotateVariants,AVASet,missing-method annotateVariants,data.frame,missing-method annotateVariants,MapperSet,BSgenome-method annotateVariants,MapperSet,missing-method
Access the amplicon data of an AVASet.	assayDataAmp
Convert an AVASet object into a VCF object	ava2vcf ava2vcf,AVASet-method
Creating an AVASet	AVASet AVASet,character,character,missing,missing,missing,missing,missing-method AVASet,character,missing,character,character,character,character,character-method AVASet,character,missing,character,character,character,missing,missing-method AVASet,character,missing,missing,missing,missing,missing,missing-method
Class to contain Amplicon Variant Analyzer Output	alignShortReads,AVASet,DNAStringSet,character-method annotateVariants,AVASet-method assayDataAmp,AVASet-method assayDataAmp<- assayDataAmp<-,AVASet,AssayData-method AVASet-class fDataAmp,AVASet-method featureDataAmp,AVASet-method featureDataAmp<- featureDataAmp<-,AVASet,AnnotatedDataFrame-method getVariantPercentages,AVASet-method htmlReport,AVASet-method referenceSequences,AVASet-method referenceSequences<- referenceSequences<-,AVASet,AlignedRead-method setVariantFilter,AVASet-method [,AVASet,ANY,ANY,ANY-method [,AVASet,ANY,ANY-method
Amplicon Variant Analyzer data import	avaSetExample
Amplicon Variant Analyzer data import	avaSetFiltered
AVASet variant annotations	avaSetFiltered_annot
Absolute And Relative Frequency Of The Four Bases.	baseFrequency baseFrequency,DNAStringSet-method baseFrequency,SFFContainer-method baseFrequency,ShortRead-method
Plot A Histogram Of The Base Qualities.	baseQualityHist baseQualityHist,QualityScaledDNAStringSet-method baseQualityHist,SFFContainer-method baseQualityHist,ShortReadQ-method
Statistics Of Base Quality	baseQualityStats baseQualityStats,QualityScaledDNAStringSet-method baseQualityStats,SFFContainer-method baseQualityStats,ShortReadQ-method
Putative breakpoints of chimeric reads	breakpoints
Class "Breakpoints"	alignedReadsC1 alignedReadsC1,Breakpoints-method alignedReadsC1<- alignedReadsC1<-,Breakpoints,list-method alignedReadsC2 alignedReadsC2,Breakpoints-method alignedReadsC2<- alignedReadsC2<-,Breakpoints,list-method Breakpoints-class commonAlignC1 commonAlignC1,Breakpoints-method commonAlignC1<- commonAlignC1<-,Breakpoints,list-method commonAlignC2 commonAlignC2,Breakpoints-method commonAlignC2<- commonAlignC2<-,Breakpoints,list-method commonBpsC1 commonBpsC1,Breakpoints-method commonBpsC1<- commonBpsC1<-,Breakpoints,list-method commonBpsC2 commonBpsC2,Breakpoints-method commonBpsC2<- commonBpsC2<-,Breakpoints,list-method length,Breakpoints-method mergeBreakpoints,Breakpoints,missing,list-method mergeBreakpoints,Breakpoints,missing,missing-method mergeBreakpoints,Breakpoints,numeric,missing-method names,Breakpoints-method names<-,Breakpoints,ANY-method plotChimericReads,Breakpoints-method seqsC1 seqsC1,Breakpoints-method seqsC1<- seqsC1<-,Breakpoints,list-method seqsC2 seqsC2,Breakpoints-method seqsC2<- seqsC2<-,Breakpoints,list-method [,Breakpoints,ANY,ANY,ANY-method [,Breakpoints,ANY,ANY-method
Calculate transition transversion ratio	calculateTiTv calculateTiTv,AVASet-method calculateTiTv,MapperSet-method
Custom capture array design	captureArray
Sequence Complexity Using The DUST Algorithm	complexity.dust complexity.dust,DNAStringSet-method complexity.dust,SFFContainer-method complexity.dust,ShortRead-method
Sequence Complexity Using The Shannon-Wiener Algorithm	complexity.entropy complexity.entropy,DNAStringSet-method complexity.entropy,SFFContainer-method complexity.entropy,ShortRead-method
Basic functions for CIGAR strings	convertCigar extendedCIGARToList listToExtendedCIGAR
Computes the coverage restricted to the target region.	coverageOnTarget coverageOnTarget,list,GRanges-method
Performs MID/Multiplex filtering	demultiplexReads demultiplexReads,XStringSet,XStringSet,missing,logical-method demultiplexReads,XStringSet,XStringSet,missing,missing-method demultiplexReads,XStringSet,XStringSet,numeric,logical-method demultiplexReads,XStringSet,XStringSet,numeric,missing-method
Clustering and consensus breakpoint detection for chimeric reads	detectBreakpoints detectBreakpoints,list-method
Dinucleotide Odds Ratio	dinucleotideOddsRatio dinucleotideOddsRatio,DNAStringSet-method dinucleotideOddsRatio,SFFContainer-method dinucleotideOddsRatio,ShortRead-method
Access the amplicon data of an AVASet.	fDataAmp
Access the amplicon data of an AVASet	featureDataAmp
Extract chimeric reads and apply filtering steps to remove artificial chimeric reads.	filterChimericReads filterChimericReads,list,IntegerRangesList,DNAString,missing,missing-method filterChimericReads,list,IntegerRangesList,DNAString,numeric,numeric-method filterChimericReads,list,IntegerRangesList,missing,missing,missing-method filterChimericReads,list,IntegerRangesList,missing,numeric,numeric-method filterChimericReads,list,missing,DNAString,missing,missing-method filterChimericReads,list,missing,DNAString,numeric,numeric-method filterChimericReads,list,missing,missing,missing,missing-method filterChimericReads,list,missing,missing,numeric,numeric-method
Create A Barplot Of The Flow Intensities	flowgramBarplot flowgramBarplot,SFFRead-method
Calculate The Overall GC-Content	gcContent gcContent,DNAStringSet-method gcContent,SFFContainer-method gcContent,ShortRead-method
GC-Content Histogram	gcContentHist gcContentHist,DNAStringSet-method gcContentHist,SFFContainer-method gcContentHist,ShortRead-method
GC-Content Per Position	gcPerPosition gcPerPosition,DNAStringSet-method gcPerPosition,SFFContainer-method gcPerPosition,ShortRead-method
Retrieve GS multiplex sequences	genomeSequencerMIDs genomeSequencerMIDs,character-method genomeSequencerMIDs,missing-method
Import reads from an Amplicon Variant Analyzer project	getAlignedReads getAlignedReads,AVASet-method
Get amino acid abbreviations	getAminoAbbr
Variant coverage	getVariantPercentages
Create A Histogram Of The Homopolymer Stretches	homopolymerHist homopolymerHist,SFFRead-method
HTML-Report Builder for the AVASet and MapperSet	htmlReport
Creating a MapperSet	MapperSet MapperSet,character-method
Class to Contain GS Reference Mapper Output	annotateVariants,MapperSet-method getReadStatus getReadStatus,MapperSet-method getVariantPercentages,MapperSet-method htmlReport,MapperSet-method MapperSet-class setVariantFilter,MapperSet-method
GS Reference Mapper data import	mapperSetExample
Identify and merge related breakpoints caused by the same variant.	mergeBreakpoints
Example data for 'plotVariants'	mutationInfo
Nucleotide Charts	nucleotideCharts nucleotideCharts,DNAStringSet-method nucleotideCharts,SFFContainer-method nucleotideCharts,ShortRead-method
Creates a plot visualizing the number of reads per amplicon	plotAmpliconCoverage plotAmpliconCoverage,AVASet,character,logical-method plotAmpliconCoverage,AVASet,character,missing-method plotAmpliconCoverage,AVASet,missing,logical-method plotAmpliconCoverage,AVASet,missing,missing-method
Plots chimeric reads	plotChimericReads
Plots variant positions	plotVariants plotVariants,AnnotatedVariants,character-method plotVariants,data.frame,character-method
Create an AVA style variation frequency plot	plotVariationFrequency plotVariationFrequency,character,numeric-method
Boxplot Of The Quality For Each Position	positionQualityBoxplot positionQualityBoxplot,QualityScaledDNAStringSet-method positionQualityBoxplot,SFFContainer-method positionQualityBoxplot,ShortReadQ-method
Function To Create A Quality Report In PDF Format	qualityReportSFF
Histogram Of The Read Lengths	readLengthHist readLengthHist,DNAStringSet-method readLengthHist,SFFContainer-method readLengthHist,ShortRead-method
Statistics For The Read Lengths	readLengthStats readLengthStats,DNAStringSet-method readLengthStats,SFFContainer-method readLengthStats,ShortRead-method
Function To Read In Roche's .sff Files	readSFF
Check for each read whether it aligns within the given region.	readsOnTarget readsOnTarget,list,GRanges-method
Access the reference sequences of an AVASet	referenceSequences
Example data for 'plotVariants'	regions
Remove linker sequences located at the start of short reads	removeLinker removeLinker,XStringSet,DNAString,logical,numeric,numeric-method removeLinker,XStringSet,DNAString,missing,missing,missing-method
Retrieve NimbleGen's sequence capture linkers	sequenceCaptureLinkers sequenceCaptureLinkers,character-method sequenceCaptureLinkers,missing-method
A Histogram Of The Sequence Qualities	sequenceQualityHist sequenceQualityHist,QualityScaledDNAStringSet-method sequenceQualityHist,SFFContainer-method sequenceQualityHist,ShortReadQ-method
Filters output of variant information	setVariantFilter
Write A SFFContainer Object To A FASTQ File	sff2fastq sff2fastq,SFFContainer-method
Class '"SFFContainer"'	addRead addRead,SFFContainer,SFFRead-method clipAdapterLeft clipAdapterLeft,SFFContainer-method clipAdapterLeft<- clipAdapterLeft<-,SFFContainer,numeric-method clipAdapterRight clipAdapterRight,SFFContainer-method clipAdapterRight<- clipAdapterRight<-,SFFContainer,numeric-method clipQualityLeft clipQualityLeft,SFFContainer-method clipQualityLeft<- clipQualityLeft<-,SFFContainer,numeric-method clipQualityRight clipQualityRight,SFFContainer-method clipQualityRight<- clipQualityRight<-,SFFContainer,numeric-method flowChars flowChars,SFFContainer-method flowChars<- flowChars<-,SFFContainer,character-method flowgramFormat flowgramFormat,SFFContainer-method flowgramFormat<- flowgramFormat<-,SFFContainer,numeric-method flowgrams flowgrams,SFFContainer-method flowgrams<- flowgrams<-,SFFContainer,list-method flowIndexes flowIndexes,SFFContainer-method flowIndexes<- flowIndexes<-,SFFContainer,list-method getRead getRead,SFFContainer,character-method keySequence keySequence,SFFContainer-method keySequence<- keySequence<-,SFFContainer,character-method name name,SFFContainer-method name<- name<-,SFFContainer,character-method reads reads,SFFContainer-method reads<- reads<-,SFFContainer,QualityScaledDNAStringSet-method SFFContainer SFFContainer-class [,SFFContainer,ANY,ANY,ANY-method [,SFFContainer,ANY,ANY-method
Class '"SFFRead"'	clipAdapterLeft,SFFRead-method clipAdapterLeft<-,SFFRead,numeric-method clipAdapterRight,SFFRead-method clipAdapterRight<-,SFFRead,numeric-method clipQualityLeft,SFFRead-method clipQualityLeft<-,SFFRead,numeric-method clipQualityRight,SFFRead-method clipQualityRight<-,SFFRead,numeric-method flowChars,SFFRead-method flowChars<-,SFFRead,character-method flowgram flowgram,SFFRead-method flowgram<- flowgram<-,SFFRead,numeric-method flowgramFormat,SFFRead-method flowgramFormat<-,SFFRead,numeric-method flowIndexes,SFFRead-method flowIndexes<-,SFFRead,numeric-method keySequence,SFFRead-method keySequence<-,SFFRead,character-method name,SFFRead-method name<-,SFFRead,character-method quality,SFFRead-method quality<- quality<-,SFFRead,BString-method read read,SFFRead-method read<- read<-,SFFRead,QualityScaledDNAStringSet-method SFFRead SFFRead-class
Example data for 'plotVariants'	variants
Function To Write Files In Roche's .sff Format	writeSFF