Accurate, high-resolution sample inference from amplicon sequencing data

Documentation for package ‘dada2’ version 1.0.3

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dada2-package	DADA2 package
assignTaxonomy	Classifies sequences against reference training dataset.
collapseNoMismatch	Combine together sequences that are identical up to shifts and/or length.
dada	High resolution sample inference from amplicon data.
dada-class	The object class returned by 'dada'
derep-class	A class representing dereplicated sequences
derepFastq	Read in and dereplicate a fastq file.
errBalancedF	An empirical error matrix.
errBalancedR	An empirical error matrix.
errExtremeF	An empirical error matrix.
errExtremeR	An empirical error matrix.
errHmpF	An empirical error matrix.
errHmpR	An empirical error matrix.
evaluate_kmers	Generate the kmer-distance and the alignment distance from the given set of sequences.
fastqFilter	Filter and trim a fastq file.
fastqPairedFilter	Filters and trims paired forward and reverse fastq files.
getDadaOpt	Get DADA options
getSequences	Get vector of sequences from input object.
getUniques	Get the uniques-vector from the input object.
inflateErr	Inflates an error rate matrix by a specified factor, while accounting for saturation.
isBimera	Determine if input sequence is a bimera of putative parent sequences.
isBimeraDenovo	Identify bimeras from collections of unique sequences.
isPhiX	Determine if input sequence(s) match the phiX genome.
isShiftDenovo	Identify sequences that are identical to a more abundant sequence up to an overall shift.
loessErrfun	Use a loess fit to estimate error rates from transition counts.
makeSequenceTable	Construct a sample-by-sequence observation matrix.
mergePairs	Merge denoised forward and reverse reads.
mergePairsByID	Merge forward and reverse reads after DADA denoising, even if reads were not originally ordered together.
nwalign	Needlman-Wunsch alignment.
nwhamming	Hamming distance after Needlman-Wunsch alignment.
plotComplementarySubstitutions	Plot Substitution Pairs from DADA Result
plotErrors	Plot observed error rates after denoising.
plotQualityProfile	Plot quality profile of a fastq file.
removeBimeraDenovo	Remove bimeras from collections of unique sequences.
setDadaOpt	Set DADA options
show-method	method extensions to show for dada2 objects.
tperr1	An empirical error matrix.
uniques-vector	The named integer vector format used to represent collections of unique DNA sequences.
uniquesToFasta	Write a uniques vector to a FASTA file