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

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Documentation for package ‘R453Plus1Toolbox’ version 1.57.0

• 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"'