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Import DADA2 data

Source: R/importers-MbioDataset.R
importDADA2.Rd

Import data from DADA2 results to MbioDataset. There is some loss of granularity in this process. It results in a simpler and more performant object which is compliant with the MicrobiomeDB infrastructure. See mia::makeTreeSEFromDADA2 for documentation.

Usage

importDADA2(
  normalizationMethod = c("TSS", "none"),
  keepRawValues = c(TRUE, FALSE),
  verbose = c(TRUE, FALSE),
  ...
)

Arguments

normalizationMethod

Normalization method to use on they assay data. Options are "none" and "TSS". Applying TSS normalization to absolute taxonomic abundances produces relative taxonomic abundances. Default is "TSS".

keepRawValues

Keep the raw assay values as well as the normalized values.

verbose

Print messages

...

Arguments to pass to mia::makeTreeSEFromDADA2

Value

A MbioDataset

Examples

fnF <- system.file("extdata", "sam1F.fastq.gz", package="dada2")
fnR = system.file("extdata", "sam1R.fastq.gz", package="dada2")
dadaF <- dada2::dada(fnF, selfConsist=TRUE)
#> Initializing error rates to maximum possible estimate.
#> selfConsist step 1 .
#>    selfConsist step 2
#>    selfConsist step 3
#>    selfConsist step 4
#> Convergence after  4  rounds.
dadaR <- dada2::dada(fnR, selfConsist=TRUE)
#> Initializing error rates to maximum possible estimate.
#> selfConsist step 1 .
#>    selfConsist step 2
#>    selfConsist step 3
#>    selfConsist step 4
#> Convergence after  4  rounds.

mbioDataset <- importDADA2(
     normalizationMethod = "none", 
     keepRawValues = TRUE, 
     verbose = TRUE, 
     dadaF, 
     fnF, 
     dadaR, 
     fnR
)