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


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Documentation for package ‘R453Plus1Toolbox’ version 1.2.2

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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"