dada_to_seq_table {dada2} | R Documentation |
Takes the
dada
result,
derepFastq
result, and
ShortReadQ-class
object
(an R representation of the original input sequence data),
and creates a data.table
in which each entry (row) contains
a unique read ID and the denoised sequence
to which it corresponds, as inferred by dada
.
dada_to_seq_table(dadaRes, derep, sr, idRegExpr = c("\\s.+$", ""), includeCol = character(0))
dadaRes |
(Required). A |
derep |
(Required).
A |
sr |
(Required). The trimmed and filtered reads
that you used as input for |
idRegExpr |
(Optional).
Exact same as for |
includeCol |
(Optional).
Exact same as for |
A data.table
in which each entry (row) contains
a unique read ID and the denoised sequence
to which it corresponds, as inferred by dada
.
exFileF = system.file("extdata", "sam1F.fastq.gz", package="dada2") show(exFileF) srF = ShortRead::readFastq(exFileF) derepF = derepFastq(exFileF) dadaF <- dada(derepF, err=tperr1, errorEstimationFunction=loessErrfun, selfConsist=TRUE) dada2:::dada_to_seq_table(dadaF, derepF, srF)