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

Documentation for package ‘R453Plus1Toolbox’ version 1.0.1

Help Pages

-- 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 --

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 --

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
filterChimericReads-method	Extract chimeric reads and apply filtering steps to remove artificial

-- 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 --

-- 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 --

Ensembl transcript information for variant plotting

-- misc --

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