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 to list construction.
c-derep-methodChange concatenation to list construction.
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'
dada_to_seq_tableMap denoised sequence to each read.
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.
errExtremeFAn empirical error matrix.
errExtremeRAn empirical error matrix.
errHmpFAn empirical error matrix.
errHmpRAn 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_SilvaThis function creates the dada2 assignTaxonomy training fasta...
mergePairsMerge denoised forward and reverse reads.
mergePairsByIDMerge forward and reverse reads after DADA denoising, even if...
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...
plotErrorsPlot observed and estimated error rates.
plotQualityProfilePlot quality profile of a fastq file.
qtables2Internal tables function
removeBimeraDenovoRemove bimeras from collections of unique sequences.
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. 1, 2018, 2:28 a.m.