Read in a taxonomy file and parse it to a wide dataframe

Usage

read_tax(taxonomy_filename, sep = "\t")

Arguments

taxonomy_filename: filename of taxonomy file
sep: Character that separates fields of the taxonomy file. (Default: \t).

Value

dataframe of taxonomic labels, formatted by parse_tax()

Author

Nick Lesniak, nlesniak@umich.edu

Kelly Sovacool, sovacool@umich.edu

Examples

taxonomy_filepath <- system.file("extdata",
  "test.taxonomy",
  package = "schtools"
)
taxonomy_tbl <- read_tax(taxonomy_filepath)
head(taxonomy_tbl)
#> # A tibble: 6 × 10
#>   otu      otu_label tax_otu_label  label_html kingdom phylum class order family
#>   <chr>    <chr>     <chr>          <chr>      <chr>   <chr>  <chr> <chr> <chr> 
#> 1 Otu0001  OTU 1     Bacteroides (… <i>Bacter… Bacter… Bacte… Bact… Bact… Bacte…
#> 2 Otu0003  OTU 3     Porphyromonad… <i>Porphy… Bacter… Bacte… Bact… Bact… Porph…
#> 3 Otu0004  OTU 4     Porphyromonad… <i>Porphy… Bacter… Bacte… Bact… Bact… Porph…
#> 4 Otu00008 OTU 8     Enterobacteri… <i>Entero… Bacter… Prote… Gamm… Ente… Enter…
#> 5 Otu0044  OTU 44    Bacteria (OTU… <i>Bacter… Bacter… Bacte… Bact… Bact… Bacte…
#> 6 Otu0056  OTU 56    Bacteria (OTU… <i>Bacter… Bacter… Bacte… Bact… Bact… Bacte…
#> # ℹ 1 more variable: genus <chr>