Man pages for R453Plus1Toolbox
A package for importing and analyzing data from Roche's Genome Sequencer System
| alignShortReads | Exact alignment of DNA sequences against a reference |
| AnnotatedVariants-class | Class "AnnotatedVariants" |
| annotateVariants | Adds genomic information to variants |
| assayDataAmp | Access the amplicon data of an AVASet. |
| ava2vcf | Convert an AVASet object into a VCF object |
| AVASet | Creating an AVASet |
| AVASet-class | Class to contain Amplicon Variant Analyzer Output |
| avaSetExample | Amplicon Variant Analyzer data import |
| avaSetFiltered | Amplicon Variant Analyzer data import |
| avaSetFiltered_annot | AVASet variant annotations |
| baseFrequency | Absolute And Relative Frequency Of The Four Bases. |
| baseQualityHist | Plot A Histogram Of The Base Qualities. |
| baseQualityStats | Statistics Of Base Quality |
| breakpoints | Putative breakpoints of chimeric reads |
| Breakpoints-class | Class "Breakpoints" |
| calculateTiTv | Calculate transition transversion ratio |
| captureArray | Custom capture array design |
| complexity.dust | Sequence Complexity Using The DUST Algorithm |
| complexity.entropy | Sequence Complexity Using The Shannon-Wiener Algorithm |
| convertCigar | Basic functions for CIGAR strings |
| coverageOnTarget | Computes the coverage restricted to the target region. |
| demultiplexReads | Performs MID/Multiplex filtering |
| detectBreakpoints | Clustering and consensus breakpoint detection for chimeric... |
| dinucleotideOddsRatio | Dinucleotide Odds Ratio |
| fDataAmp | Access the amplicon data of an AVASet. |
| featureDataAmp | Access the amplicon data of an AVASet |
| filterChimericReads | Extract chimeric reads and apply filtering steps to remove... |
| flowgramBarplot | Create A Barplot Of The Flow Intensities |
| gcContent | Calculate The Overall GC-Content |
| gcContentHist | GC-Content Histogram |
| gcPerPosition | GC-Content Per Position |
| genomeSequencerMIDs | Retrieve GS multiplex sequences |
| getAlignedReads | Import reads from an Amplicon Variant Analyzer project |
| getAminoAbbr | Get amino acid abbreviations |
| getVariantPercentages | Variant coverage |
| homopolymerHist | Create A Histogram Of The Homopolymer Stretches |
| htmlReport | HTML-Report Builder for the AVASet and MapperSet |
| MapperSet | Creating a MapperSet |
| MapperSet-class | Class to Contain GS Reference Mapper Output |
| mapperSetExample | GS Reference Mapper data import |
| mergeBreakpoints | Identify and merge related breakpoints caused by the same... |
| mutationInfo | Example data for 'plotVariants' |
| nucleotideCharts | Nucleotide Charts |
| plotAmpliconCoverage | Creates a plot visualizing the number of reads per amplicon |
| plotChimericReads | Plots chimeric reads |
| plotVariants | Plots variant positions |
| plotVariationFrequency | Create an AVA style variation frequency plot |
| positionQualityBoxplot | Boxplot Of The Quality For Each Position |
| qualityReportSFF | Function To Create A Quality Report In PDF Format |
| readLengthHist | Histogram Of The Read Lengths |
| readLengthStats | Statistics For The Read Lengths |
| readSFF | Function To Read In Roche's .sff Files |
| readsOnTarget | Check for each read whether it aligns within the given... |
| referenceSequences | Access the reference sequences of an AVASet |
| regions | Example data for 'plotVariants' |
| removeLinker | Remove linker sequences located at the start of short reads |
| sequenceCaptureLinkers | Retrieve NimbleGen's sequence capture linkers |
| sequenceQualityHist | A Histogram Of The Sequence Qualities |
| setVariantFilter | Filters output of variant information |
| sff2fastq | Write A SFFContainer Object To A FASTQ File |
| SFFContainer-class | Class '"SFFContainer"' |
| SFFRead-class | Class '"SFFRead"' |
| variants | Example data for 'plotVariants' |
| writeSFF | Function To Write Files In Roche's .sff Format |
