DADA2: Exact Sample Inference from Amplicon Sequencing Data


[Up] [Top]

Documentation for package ‘dada2’ version 0.10.1

Help Pages

dada2-package DADA2 package
assignTaxonomy assignTaxonomy assigns taxonomy to provided sequences.
collapseNoMismatch Collapse 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'
dada_to_seq_table Map denoised sequence to each read.
derep-class derep - A class representing dereplicated sequences
derepFastq Read 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 fastqFilter filters and trims fastq files.
fastqPairedFilter fastqPairedFilter filters and trims paired forward and reverse fastq files.
getDadaOpt Get DADA options
getSequences Get vector of sequences.
getUniques Get the "uniques vector": Integer vector named by sequence and valued by abundance.
inflateErr Inflates an error rate matrix by a specified factor accounting for saturation.
isBimera Determine if input sequence is a bimera of putative parent sequences.
isBimeraDenovo Identify bimeras de-novo from collections of unique sequences.
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 paired forward and reverse reads after DADA denoising.
mergePairsByID Merge forward and reverse reads after DADA denoising, even if reads were not originally ordered together.
nwalign Needlman-Wunsch alignment with ends-free gapping.
nwhamming Hamming distance after Needlman-Wunsch alignment with ends-free gapping.
plotComplementarySubstitutions Plot Substitution Pairs from DADA Result
plotErrors Plot error rates after dada processing.
setDadaOpt Set DADA options
show-method method extensions to show for dada2 objects.
tperr1 An empirical error matrix.
uniquesToFasta Write a uniques vector to a FASTA file