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Last data update: 2014.03.03

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Results 1 - 10 of 55 found.
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AVASet-class (Package: R453Plus1Toolbox) : Class to contain Amplicon Variant Analyzer Output

Container to store data imported from a project of Roche's Amplicon Variant Analyzer Software. It stores all information into an extended version of the Biobase ExpressionSet.

● Data Source: BioConductor
● Keywords: classes
● Alias: AVASet-class, [,AVASet,ANY,ANY-method, alignShortReads,AVASet,DNAStringSet,character-method, annotateVariants,AVASet-method, assayDataAmp,AVASet-method, assayDataAmp<-, assayDataAmp<-,AVASet,AssayData-method, 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
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AVASet (Package: R453Plus1Toolbox) : Creating an AVASet

This function imports a project of Roche's Amplicon Variant Analyzer (AVA) Software. It stores all information into an extended version of the Biobase eSet.

● Data Source: BioConductor
● Keywords:
● Alias: 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
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AnnotatedVariants-class (Package: R453Plus1Toolbox) : Class "AnnotatedVariants"

A class for storing annotation about variants. An object of this class is returned by the method annotateVariants. The class has not been designed to be created by users directly.

● Data Source: BioConductor
● Keywords: classes
● Alias: AnnotatedVariants-class, annotatedVariants, annotatedVariants,AnnotatedVariants-method, annotatedVariants<-,AnnotatedVariants,list-method, names,AnnotatedVariants-method, names<-,AnnotatedVariants,character-method
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Breakpoints-class (Package: R453Plus1Toolbox) : Class "Breakpoints"

Container to store chimeric reads that were clustered to putative breakpoints indicating structural variants. Related information like breakpoint position or alignment information about the chimeric reads is stored as well.

● Data Source: BioConductor
● Keywords: classes
● Alias: Breakpoints-class, [,Breakpoints,ANY,ANY-method, alignedReadsC1, alignedReadsC1,Breakpoints-method, alignedReadsC1<-, alignedReadsC1<-,Breakpoints,list-method, alignedReadsC2, alignedReadsC2,Breakpoints-method, alignedReadsC2<-, alignedReadsC2<-,Breakpoints,list-method, 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
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MapperSet-class (Package: R453Plus1Toolbox) : Class to Contain GS Reference Mapper Output

Container to store data imported from a project of Roche's GS Reference Mapper Software. It stores all information into a Biobase ExpressionSet.

● Data Source: BioConductor
● Keywords: classes
● Alias: MapperSet-class, annotateVariants,MapperSet-method, getReadStatus, getReadStatus,MapperSet-method, getVariantPercentages,MapperSet-method, htmlReport,MapperSet-method, setVariantFilter,MapperSet-method
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MapperSet (Package: R453Plus1Toolbox) : Creating a MapperSet

This function imports a project of Roche's GS Reference Mapper Software. It stores all information into an instance of the Biobase ExpressionSet.

● Data Source: BioConductor
● Keywords:
● Alias: MapperSet, MapperSet,character-method
● 0 images

SFFContainer-class (Package: R453Plus1Toolbox) : Class code{"SFFContainer"

This class is a container for data from files in Roche's Standard Flowgram Format (SFF).

● Data Source: BioConductor
● Keywords: classes
● Alias: SFFContainer, SFFContainer-class, [,SFFContainer,ANY,ANY-method, 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, flowIndexes, flowIndexes,SFFContainer-method, flowIndexes<-, flowIndexes<-,SFFContainer,list-method, flowgramFormat, flowgramFormat,SFFContainer-method, flowgramFormat<-, flowgramFormat<-,SFFContainer,numeric-method, flowgrams, flowgrams,SFFContainer-method, flowgrams<-, flowgrams<-,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
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SFFRead-class (Package: R453Plus1Toolbox) : Class code{"SFFRead"

This class is a container for a single read from files in Roche's Standard Flowgram Format (SFF).

● Data Source: BioConductor
● Keywords: classes
● Alias: SFFRead, SFFRead-class, 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, flowIndexes,SFFRead-method, flowIndexes<-,SFFRead,numeric-method, flowgram, flowgram,SFFRead-method, flowgram<-, flowgram<-,SFFRead,numeric-method, flowgramFormat,SFFRead-method, flowgramFormat<-,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
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alignShortReads (Package: R453Plus1Toolbox) : Exact alignment of DNA sequences against a reference

This method aligns given sequences against a given reference genome using the matchPDict method. Only exact (no errors) and unique matches are returned.

● Data Source: BioConductor
● Keywords: alignShortReads
● Alias: 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
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annotateVariants (Package: R453Plus1Toolbox) : Adds genomic information to variants

This method annotates given genomic variants (mutations). Annotation includes affected genes, exons and codons. Resulting amino acid changes are returned as well as dbSNP identifiers, if the mutation is already known. All information is fetched from Ensembl via biomaRt using the datasets hsapiens_gene_ensembl and hsapiens_snp.

● Data Source: BioConductor
● Keywords: annotateVariants
● Alias: annotateVariants, annotateVariants,AVASet,missing-method, annotateVariants,MapperSet,BSgenome-method, annotateVariants,MapperSet,missing-method, annotateVariants,data.frame,missing-method
● 0 images