import_dada2 {MicrobiotaProcess} | R Documentation

## Import function to load the feature table and taxanomy table of dada2

### Description

the function can import the ouput of dada2, and generated the phyloseq obj contained the argument class.

### Usage

    import_dada2(
      seqtab,
      taxatab = NULL,
      reftree = NULL,
      sampleda = NULL,
      btree = FALSE,
      ...
    )

### Arguments

`seqtab` | matrix, feature table, the output of `removeBimeraDenovo`.
`taxatab` | matrix, a taxonomic table, the output of `assignTaxonomy`, or the ouput of `addSpecies`.
`reftree` | phylo or character, the phylo class of tree, or the tree file.
`sampleda` | data.frame or character, the data.frame of sample information, or the file of sample information, nrow samples X ncol factors.
`btree` | logical, whether building the tree, default is FALSE.
`...,` | additional parameters, see also `build_tree`.

### Value

phyloseq class contained the argument class.

### Author(s)

Shuangbin Xu

### Examples

    seqtabfile <- system.file("extdata", "seqtab.nochim.rds",
                              package="MicrobiotaProcess")
    taxafile <- system.file("extdata", "taxa_tab.rds",
                            package="MicrobiotaProcess")
    seqtab <- readRDS(seqtabfile)
    taxa <- readRDS(taxafile)
    sampleda <- system.file("extdata", "mouse.time.dada2.txt",
                            package="MicrobiotaProcess")
    ps <- import_dada2(seqtab=seqtab, taxatab=taxa,
                       sampleda=sampleda)
    ps

[Package MicrobiotaProcess version 1.2.2 Index]