This is an example of an link{AVASet-class} object containing the output of Roche's Amplicon Variant Analyzer Software. It consists of 6 samples, 4 amplicons and 259 variants.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: avaSetExample
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This is an example of an link{AVASet-class} object containing the output of Roche's Amplicon Variant Analyzer Software. It consists of 6 samples, 4 amplicons and 4 variants. The variants were previously filtered according to the amplicon coverage (see setVariantFilter for details about filtering an AVASet object).
● Data Source:
BioConductor
● Keywords: datasets
● Alias: avaSetFiltered
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These are example annotations for 4 variants of an AVASet (try data(avaSetFiltered) to retrieve the corresponding link{AVASet-class} object). The annotations include affected genes, exons and codons as well as resulting amino acid changes and dbSNP identifiers (if the mutation is already known).
● Data Source:
BioConductor
● Keywords: datasets
● Alias: avaSetFiltered_annot
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This example holds two consensus (pathogenic and reciproce) breakpoints of 12 chimeric reads indicating an inversion on chromosome 16. The Breakpoints object gives access to the breakpoint locations as well as alignment information for each of the 12 reads.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: breakpoints
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Design of a custom Roche NimbleGen 385k capture array. The array captures short segments corresponding to all exon regions of 92 distinct target genes (genome build hg19). In addition, contiguous genomic regions were represented for three additional genes, i.e. CBFB, MLL, and RUNX1.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: captureArray
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This is an example of an link{MapperSet-class} object containing the output of Roche's GS Reference Mapper Software. It consists of 3 samples and 111 variants.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: mapperSetExample
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This data.frame is part of the vignette example of the plotVariants function. It contains annotations for the different mutations occurring in the example data. It has columns "mutation", "legend" and "color".
● Data Source:
BioConductor
● Keywords: datasets
● Alias: mutationInfo
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This data.frame is part of the vignette example of the plotVariants function. It has the columns "name", "start", "end" and "color". The plot will highlight these regions with the given colors and print their name in the legend.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: regions
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This data.frame is part of the vignette example of the plotVariants function. It has the columns "label", "pos" "mutation" and "color" specifying an annotation for each mutation, its position, the mutation type and an individual color. The position is given as amino acids / codons.
● Data Source:
BioConductor
● Keywords: datasets
● Alias: variants
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