R/allClasses.R
, R/show-methods.R
, R/subset-methods.R
MultiAmplicon-class.Rd
The MultiAmplicon class is a container that stores at least primer
pairs, read files and progressively processed data in an 'amplicon
x samples' format. The slots in this object are incrementally
filled with by running wrappers functions (mostly around functions
from the dada2
package). The object is treated (subsetted
etc.) like a (pseudo) matrix, colums are samples, rows are
different amplicons.
Subsetting for MultiAmplicon objects should conveniently subset all (potentially) filled slots
MultiAmplicon( PrimerPairsSet = PrimerPairsSet(), PairedReadFileSet = PairedReadFileSet(), .Data = matrix(ncol = 0, nrow = 0), stratifiedFiles = list(), sampleData = new("sample_data", data.frame(row.names = names(PairedReadFileSet), readsF = PairedReadFileSet@readsF, readsR = PairedReadFileSet@readsF)), derep = list(), dada = list(), mergers = list(), sequenceTable = list(), sequenceTableNoChime = list(), taxonTable = list() ) getPrimerPairsSet(MA) getPairedReadFileSet(MA) getRawCounts(MA) getStratifiedFilesF(MA, simplify = TRUE) getStratifiedFilesR(MA, simplify = TRUE) getDerepF(MA, simplify = TRUE) getDerepR(MA, simplify = TRUE) getDadaF(MA, simplify = TRUE) getDadaR(MA, simplify = TRUE) getMergers(MA, simplify = TRUE) getSequenceTable(MA, simplify = TRUE) getSequenceTableNoChime(MA, simplify = TRUE) getTaxonTable(MA, simplify = TRUE) getSequencesFromTable(MA) # S4 method for MultiAmplicon getSequencesFromTable(MA) # S4 method for MultiAmplicon show(object) # S4 method for MultiAmplicon,index,index,ANY [(x, i, j, ..., drop = FALSE) # S4 method for MultiAmplicon,index,missing,ANY [(x, i, j, ..., drop = FALSE) # S4 method for MultiAmplicon,missing,index,ANY [(x, i, j, ..., drop = FALSE)
PrimerPairsSet | a set of primer pairs specifiying your
amplicons see |
---|---|
PairedReadFileSet | a set of paired end sequencing data files
|
.Data | Users should not supply this parameter, the slot
is created by |
stratifiedFiles | Users should not supply this parameter, the
slot is created by |
sampleData | Users should not supply this parameter. It's
filled with a sample_data object from
|
derep | Users should not supply this parameter, the slot is
created by |
dada | Users should not supply this parameter, the slot is
created by |
mergers | Users should not supply this parameter, the slot is
created by |
sequenceTable | Users should not supply this parameter, the
slot is created by |
sequenceTableNoChime | Users should not supply this parameter,
the slot is created by |
taxonTable | Users should not supply this parameter, the slot
is created by |
MA | MultiAmplicon-class object |
simplify | Should a list of objects be simplified to only one object if it has length one? |
object | A |
x | MultiAmplicon-class object |
i | numeric, logical or names vector for subsetting rows (== amplicons) |
j | numeric, logical or names vector for subsetting columns (== read files, corresponding usually to samples) |
... | not used |
drop | should not be used |
MultiAmplicon
: Constructor for
MultiAmplicon-class
PrimerPairsSet
The primer pairs used in your experiment to
specify amplicons stored in a
PrimerPairsSet-class
object.
PairedReadFileSet
The (quality filtered) fastq files (one file pair for each sample) that store your sequencing data.
.Data
A numeric matrix of sequencing read counts per
amplicon and sample. Created by the function
sortAmplicons
in the MultiAmplicon pipeline.
sampleData
A sample_data object from
phyloseq
. The slot is created from
sample names (names of the PrimerPairsSet
, which
have tto be the same as colnames(MA)
). More data can be
added by addSampleData
.
stratifiedFiles
temporary files as a result of stratifying
into amplicons and samples using the MultiAmplicon pipeline
function sortAmplicons
. Forward (sometimes
called R1) and reverse (sometimes called R2) files are stored
as a (amplicons x samples) matrix of
PairedReadFileSet-class
objects.
derep
A list of PairedDerep-class
objects
containing pairs of derep-class objects created by
dada2
’s derepFastq
function or
withing the MultiAmplicon pipeline by
derepMulti
.
dada
A list of PairedDada-class
object
containing pairs of dada-class objects created by
dada2
’s dada
function. Within the
MultiAmplicon pipeline this slot is filled by
dadaMulti
.
mergers
A list of objects containing merged pairs of forward
and reverse reads as created by by dada2
’s
mergePairs
function. Within the
MultiAmplicon pipeline this slot is filled by
mergeMulti
.
sequenceTable
A list of matrix objects created by
dada2
’s makeSequenceTable
.
Samples (in rows) and amplified sequence variants (ASVs) in
columns. Within the MultiAmplicon pipeline this slot is
filled by makeSequenceTableMulti
.
sequenceTableNoChime
A list of matrix objects created by
dada2
’s removeBimeraDenovo
.
Samples (in rows) and ASVs screened for PCR chimeras in
columns. Within the MultiAmplicon pipeline this slot is filled
by removeChimeraMulti
.
taxonTable
A list of matrix objects created by a function
for taxonomical annotation (for example
blastTaxAnnot
. ASVs are in rows and taxnomical
ranks are in columns. MultiAmplicon(PrimerPairsSet, PairedReadFileSet)
Emanuel Heitlinger
primerF <- c("AGAGTTTGATCCTGGCTCAG", "ACTCCTACGGGAGGCAGC", "GAATTGACGGAAGGGCACC", "YGGTGRTGCATGGCCGYT") primerR <- c("CTGCWGCCNCCCGTAGG", "GACTACHVGGGTATCTAATCC", "AAGGGCATCACAGACCTGTTAT", "TCCTTCTGCAGGTTCACCTAC") PPS <- PrimerPairsSet(primerF, primerR) fastq.dir <- system.file("extdata", "fastq", package = "MultiAmplicon") fastq.files <- list.files(fastq.dir, full.names=TRUE) Ffastq.file <- fastq.files[grepl("F_filt", fastq.files)] Rfastq.file <- fastq.files[grepl("R_filt", fastq.files)] PRF <- PairedReadFileSet(Ffastq.file, Rfastq.file) MA <- MultiAmplicon(PPS, PRF) ## sort into amplicons MA1 <- sortAmplicons(MA, filedir=tempfile(pattern = "dir"))#>#>#> #> #>#>#> #> #>#>#> #> #>#>#> #> #>#>#> #> #>#>#> #> #>#>#> #> #>#>#> #> #>## Only after sorting the MultiAmplicon object is really poplated ## with sensible data, now matrix-like access to different ## amplicons (primer pairs) and different sequencing read files ## (usually samples) is implemented ## the number of amplicons (primer pairs) nrow(MA)#> [1] 0#> [1] 0## dereplication is currently not supported ## MA2 <- derepMulti(MA1) ### use dada directly after sorting MA3 <- dadaMulti(MA1, selfConsist = TRUE)#> #> #>#>#> Initializing error rates to maximum possible estimate. #> selfConsist step 1 ...... #> selfConsist step 2 #> selfConsist step 3 #> selfConsist step 4 #> selfConsist step 5 #> selfConsist step 6 #> Convergence after 6 rounds. #> Initializing error rates to maximum possible estimate. #> selfConsist step 1 ...... #> selfConsist step 2 #> selfConsist step 3 #> selfConsist step 4 #> selfConsist step 5 #> Convergence after 5 rounds.#> #> #>#>#> Initializing error rates to maximum possible estimate. #> selfConsist step 1 ..... #> selfConsist step 2 #> selfConsist step 3 #> selfConsist step 4 #> selfConsist step 5 #> selfConsist step 6 #> Convergence after 6 rounds. #> Initializing error rates to maximum possible estimate. #> selfConsist step 1 ..... #> selfConsist step 2 #> selfConsist step 3 #> selfConsist step 4 #> selfConsist step 5 #> Convergence after 5 rounds.#> #> #>#>#> Initializing error rates to maximum possible estimate. #> selfConsist step 1 .. #> selfConsist step 2 #> selfConsist step 3 #> selfConsist step 4 #> selfConsist step 5 #> Convergence after 5 rounds. #> Initializing error rates to maximum possible estimate. #> selfConsist step 1 .. #> selfConsist step 2 #> selfConsist step 3 #> selfConsist step 4 #> selfConsist step 5 #> Convergence after 5 rounds.#> #> #>#>#> Initializing error rates to maximum possible estimate. #> selfConsist step 1 ..... #> selfConsist step 2 #> selfConsist step 3 #> selfConsist step 4 #> selfConsist step 5 #> Convergence after 5 rounds. #> Initializing error rates to maximum possible estimate. #> selfConsist step 1 ..... #> selfConsist step 2 #> selfConsist step 3 #> selfConsist step 4 #> Convergence after 4 rounds.#> #>#>#> #>#>#> #>#>#> #>#>#>#>#>#>#>#>#>#>