Accurate, high-resolution sample inference from amplicon sequencing data

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Documentation for package ‘dada2’ version 1.26.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

dada2-package	DADA2 package
addSpecies	Add species-level annotation to a taxonomic table.
assignSpecies	Taxonomic assignment to the species level by exact matching.
assignTaxonomy	Classifies sequences against reference training dataset.
c-method	Change concatenation of dada-class objects to list construction.
c-method	Change concatenation of derep-class objects to list construction.
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.
fastqFilter	Filter and trim a fastq file.
fastqPairedFilter	Filters and trims paired forward and reverse fastq files.
filterAndTrim	Filter and trim fastq file(s).
getDadaOpt	Get DADA options
getErrors	Extract already computed error rates.
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.
isBimeraDenovoTable	Identify bimeras in a sequence table.
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.
learnErrors	Learns the error rates from an input list, or vector, of file names or a list of 'derep-class' objects.
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.
mergeSequenceTables	Merge two or more sample-by-sequence observation matrices.
names<--method	Deactivate renaming of dada-class objects.
names<--method	Deactivate renaming of derep-class objects.
noqualErrfun	Estimate error rates for each type of transition while ignoring quality scores.
nwalign	Needleman-Wunsch alignment.
nwhamming	Hamming distance after Needlman-Wunsch alignment.
PacBioErrfun	Estimate error rates from transition counts in PacBio CCS data.
plotComplexity	Plot sequence complexity profile of a fastq file.
plotErrors	Plot observed and estimated error rates.
plotQualityProfile	Plot quality profile of a fastq file.
rc	Reverse complement DNA sequences.
removeBimeraDenovo	Remove bimeras from collections of unique sequences.
removePrimers	Removes primers and orients reads in a consistent direction.
seqComplexity	Determine if input sequence(s) are low complexity.
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
writeFasta-method	Writes a named character vector of DNA sequences to a fasta file. Values are the sequences, and names are used for the id lines.