Man pages for dada2
Accurate, high-resolution sample inference from amplicon sequencing data

addSpeciesAdd species-level annotation to a taxonomic table.
assignSpeciesTaxonomic assignment to the species level by exact matching.
assignTaxonomyClassifies sequences against reference training dataset.
c-dada-methodChange concatenation of dada-class objects to list...
c-derep-methodChange concatenation of derep-class objects to list...
collapseNoMismatchCombine together sequences that are identical up to shifts...
dadaHigh resolution sample inference from amplicon data.
dada2-packageDADA2 package
dada-classThe object class returned by 'dada'
derep-classA class representing dereplicated sequences
derepFastaderepFasta creates a derep-class object from a fasta file, by...
derepFastqRead in and dereplicate a fastq file.
errBalancedFAn empirical error matrix.
errBalancedRAn empirical error matrix.
fastqFilterFilter and trim a fastq file.
fastqPairedFilterFilters and trims paired forward and reverse fastq files.
filterAndTrimFilter and trim fastq file(s).
getDadaOptGet DADA options
getErrorsExtract already computed error rates.
getSequencesGet vector of sequences from input object.
getUniquesGet the uniques-vector from the input object.
inflateErrInflates an error rate matrix by a specified factor, while...
isBimeraDetermine if input sequence is a bimera of putative parent...
isBimeraDenovoIdentify bimeras from collections of unique sequences.
isBimeraDenovoTableIdentify bimeras in a sequence table.
isPhiXDetermine if input sequence(s) match the phiX genome.
isShiftDenovoIdentify sequences that are identical to a more abundant...
learnErrorsLearns the error rates from an input list, or vector, of file...
loessErrfunUse a loess fit to estimate error rates from transition...
makeSequenceTableConstruct a sample-by-sequence observation matrix.
makeSpeciesFasta_RDPThis function creates the dada2 assignSpecies fasta file for...
makeSpeciesFasta_SilvaThis function creates the dada2 assignSpecies fasta file for...
makeTaxonomyFasta_RDPThis function creates the dada2 assignTaxonomy training fasta...
makeTaxonomyFasta_SilvaDEPRECATED in favor of 'makeTaxonomyFasta_SilvaNR"
makeTaxonomyFasta_SilvaNRThis function creates the dada2 assignTaxonomy training fasta...
mergePairsMerge denoised forward and reverse reads.
mergeSequenceTablesMerge two or more sample-by-sequence observation matrices.
names-set-dada-ANY-methodDeactivate renaming of dada-class objects.
names-set-derep-ANY-methodDeactivate renaming of derep-class objects.
noqualErrfunEstimate error rates for each type of transition while...
nwalignNeedleman-Wunsch alignment.
nwhammingHamming distance after Needlman-Wunsch alignment.
PacBioErrfunEstimate error rates from transition counts in PacBio CCS...
plotComplexityPlot sequence complexity profile of a fastq file.
plotErrorsPlot observed and estimated error rates.
plotQualityProfilePlot quality profile of a fastq file.
qtables2Internal tables function
rcReverse complement DNA sequences.
removeBimeraDenovoRemove bimeras from collections of unique sequences.
removePrimersRemoves primers and orients reads in a consistent direction.
seqComplexityDetermine if input sequence(s) are low complexity.
setDadaOptSet DADA options
show-methodsmethod extensions to show for dada2 objects.
tperr1An empirical error matrix.
uniquesToFastaWrite a uniques vector to a FASTA file
uniques-vectorThe named integer vector format used to represent collections...
writeFastaWrites a named character vector of DNA sequences to a fasta...
dada2 documentation built on Nov. 8, 2020, 6:48 p.m.