All functions

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>)

The central data structure of the MultiAmplicon package

PairedDada() length(<PairedDada>) `[`(<PairedDada>,<index>,<missing>,<ANY>)

PairedDada-class

length(<PairedDerep>) `[`(<PairedDerep>,<index>,<missing>,<ANY>)

PairedDerep-class

PairedReadFileSet() length(<PairedReadFileSet>) show(<PairedReadFileSet>) `[`(<PairedReadFileSet>,<index>,<missing>,<ANY>)

A class representing file paths to paired end reads.

PrimerPairsSet() length(<PrimerPairsSet>) names(<PrimerPairsSet>) show(<PrimerPairsSet>) `[`(<PrimerPairsSet>,<index>,<missing>,<ANY>)

A class representing sequences of forward and reverse primers.

addSampleData()

addSampleData

blastTaxAnnot()

blastTaxAnnot

calcPropMerged()

calcPropMerged

carnivoreSeqRuns

Download sequencing run files for a carnivore biome dataset

concatenateMultiAmplicon()

concatenateMultiAmplicon

dadaMulti()

dadaMulti

derepMulti()

derepMulti

.fillSampleTables()

.fillSampleTables

getPipelineSummary()

getPipelineSummary

makeSequenceTableMulti()

makeSequenceTableMulti

mergeMulti()

mergeMulti

plotAmpliconNumbers() plotPipelineSummary(<MultiAmplicon>) plotPipelineSummary(<data.frame>)

plotAmpliconNumbers

plotPipelineSummary()

plotPipelineSummary

removeChimeraMulti()

removeChimeraMulti

sortAmplicons()

sortAmplicons

toPhyloseq()

toPhyloseq