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MultiAmplicon() getPrimerPairsSet() getPairedReadFileSet() getRawCounts() getStratifiedFilesF() getStratifiedFilesR() getDerepF() getDerepR() getDadaF() getDadaR() getMergers() getSequenceTable() getSequenceTableNoChime() getTaxonTable() getSequencesFromTable() show(<MultiAmplicon>) `[`(<MultiAmplicon>,<index>,<index>,<ANY>) `[`(<MultiAmplicon>,<index>,<missing>,<ANY>) `[`(<MultiAmplicon>,<missing>,<index>,<ANY>)
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The central data structure of the MultiAmplicon package |
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PairedDada() length(<PairedDada>) `[`(<PairedDada>,<index>,<missing>,<ANY>)
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PairedDada-class |
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length(<PairedDerep>) `[`(<PairedDerep>,<index>,<missing>,<ANY>)
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PairedDerep-class |
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PairedReadFileSet() length(<PairedReadFileSet>) show(<PairedReadFileSet>) `[`(<PairedReadFileSet>,<index>,<missing>,<ANY>)
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A class representing file paths to paired end reads. |
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PrimerPairsSet() length(<PrimerPairsSet>) names(<PrimerPairsSet>) show(<PrimerPairsSet>) `[`(<PrimerPairsSet>,<index>,<missing>,<ANY>)
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A class representing sequences of forward and reverse primers. |
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addSampleData()
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addSampleData |
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blastTaxAnnot()
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blastTaxAnnot |
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calcPropMerged()
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calcPropMerged |
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carnivoreSeqRuns
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Download sequencing run files for a carnivore biome dataset |
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concatenateMultiAmplicon()
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concatenateMultiAmplicon |
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dadaMulti()
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dadaMulti |
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derepMulti()
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derepMulti |
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.fillSampleTables()
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.fillSampleTables |
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getPipelineSummary()
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getPipelineSummary |
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makeSequenceTableMulti()
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makeSequenceTableMulti |
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mergeMulti()
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mergeMulti |
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plotAmpliconNumbers() plotPipelineSummary(<MultiAmplicon>) plotPipelineSummary(<data.frame>)
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plotAmpliconNumbers |
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plotPipelineSummary()
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plotPipelineSummary |
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removeChimeraMulti()
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removeChimeraMulti |
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sortAmplicons()
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sortAmplicons |
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toPhyloseq()
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toPhyloseq |