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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.

For QIIME 2, metadata columns are typed numeric or categorical (logical and Date fields are categorical; dates are written as YYYY-MM-DD). For mothur, taxonomy rows use the OTU IDs from the counts file, and missing ranks are written as unclassified.

Usage

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

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

Arguments

biom

An rbiom object, or any value accepted by as_rbiom().

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_'

overwrite

Replace files that already exist? Default: FALSE

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] "Unc01yki\t24096\tBacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus;"
#> [3] "Unc53100\t23409\tBacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus;"

    unlink(tdir, recursive = TRUE)