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Export data to QIIME 2 or mothur.

Source: R/write_biom.r
export.Rd

Populates a directory with the following files, formatted according to QIIME 2 or mothur's specifications.

  • biom_counts.tsv

  • biom_metadata.tsv

  • biom_taxonomy.tsv

  • biom_tree.nwk

  • biom_seqs.fna

biom_counts.tsv will always be created. The others are dependent on whether the content is present in the biom argument.

Usage

write_mothur(biom, dir = tempfile(), prefix = "biom_")

write_qiime2(biom, dir = tempfile(), prefix = "biom_")

Arguments

biom

An rbiom object, such as from as_rbiom(). Any value accepted by as_rbiom() can also be given here.

dir

Where to save the files. If the directory doesn't exist, it will be created. Default: tempfile()

prefix

A string to prepend to each file name. Default: 'biom_'

Value

The normalized directory path that was written to (invisibly).

Examples

    library(rbiom)
    
    tdir <- tempfile()
    
    write_qiime2(hmp50, tdir, 'qiime2_')
    write_mothur(hmp50, tdir, 'mothur_')
    
    list.files(tdir)
#>  [1] "mothur_counts.tsv"   "mothur_metadata.tsv" "mothur_seqs.fna"    
#>  [4] "mothur_taxonomy.tsv" "mothur_tree.nwk"     "qiime2_counts.tsv"  
#>  [7] "qiime2_metadata.tsv" "qiime2_seqs.fna"     "qiime2_taxonomy.tsv"
#> [10] "qiime2_tree.nwk"    
    
    readLines(file.path(tdir, 'qiime2_metadata.tsv'), n = 4)
#> [1] "sample-id\tAge\tBMI\t\"Body Site\"\tSex"              
#> [2] "#q2:types\tnumeric\tnumeric\tcategorical\tcategorical"
#> [3] "HMP01\t22\t20\t\"Buccal mucosa\"\tFemale"             
#> [4] "HMP02\t24\t23\t\"Buccal mucosa\"\tMale"               
    
    readLines(file.path(tdir, 'mothur_taxonomy.tsv'), n = 3)
#> [1] "OTU\tSize\tTaxonomy"                                                                 
#> [2] "1\t24096\tBacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus"
#> [3] "2\t23409\tBacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus"
    
    unlink(tdir, recursive = TRUE)