dada_to_seq_table {dada2}R Documentation

Map denoised sequence to each read.

Description

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.

Usage

dada_to_seq_table(dadaRes, derep, sr, idRegExpr = c("\\s.+$", ""),
  includeCol = character(0))

Arguments

dadaRes

(Required). A dada-class object. The output of dada function.

derep

(Required). A derep-class object. An object returned by derepFastq(). Should be the same object that served as input to the dada function.

sr

(Required). The trimmed and filtered reads that you used as input for derepFastq, prior to running dada() on derep. More generally, this is an object that inherits from the ShortRead-class. In most cases this will be ShortReadQ-class. Objects from this class are the result of readFastq. Alternatively, this can be a character string that provides the path to your forward reads fastq file.

idRegExpr

(Optional). Exact same as for mergePairsByID.

includeCol

(Optional). Exact same as for mergePairsByID.

Value

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.

Examples

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)
[Package dada2 version 1.8.0 Index]