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Load a single parquet reference file

Source: R/readParquet.R
load_ref.Rd

'load_ref' retrieves a single parquet file by name from a designated repo and loads it into a table in R.

Usage

load_ref(ref, repo = NULL, file_path = NULL)

Arguments

ref

String: the name of a reference file as found in get_ref_info()

repo

String (optional): Hugging Face repo where the parquet files are stored. If NULL, the repo listed as the default in get_repo_info() will be selected. Default: NULL

file_path

String (optional): path to locally stored parquet file. Default: NULL

Value

A table of reference information

See also

filter, pull read_parquet

Examples

# \donttest{
 load_ref("clade_name_ref")
#> # A tibble: 11,702 × 18
#>    clade_name              clade_name_kingdom clade_name_phylum clade_name_class
#>    <chr>                   <chr>              <chr>             <chr>           
#>  1 UNCLASSIFIED            UNCLASSIFIED       NA                NA              
#>  2 k__Archaea              k__Archaea         NA                NA              
#>  3 k__Archaea|p__Candidat… k__Archaea         p__Candidatus_Th… NA              
#>  4 k__Archaea|p__Candidat… k__Archaea         p__Candidatus_Th… c__Thermoplasma…
#>  5 k__Archaea|p__Candidat… k__Archaea         p__Candidatus_Th… c__Thermoplasma…
#>  6 k__Archaea|p__Candidat… k__Archaea         p__Candidatus_Th… c__Thermoplasma…
#>  7 k__Archaea|p__Candidat… k__Archaea         p__Candidatus_Th… c__Thermoplasma…
#>  8 k__Archaea|p__Candidat… k__Archaea         p__Candidatus_Th… c__Thermoplasma…
#>  9 k__Archaea|p__Candidat… k__Archaea         p__Candidatus_Th… c__Thermoplasma…
#> 10 k__Archaea|p__Candidat… k__Archaea         p__Candidatus_Th… c__Thermoplasma…
#> # ℹ 11,692 more rows
#> # ℹ 14 more variables: clade_name_order <chr>, clade_name_family <chr>,
#> #   clade_name_genus <chr>, clade_name_species <chr>,
#> #   clade_name_terminal <chr>, NCBI_tax_id <chr>, NCBI_tax_id_kingdom <chr>,
#> #   NCBI_tax_id_phylum <chr>, NCBI_tax_id_class <chr>, NCBI_tax_id_order <chr>,
#> #   NCBI_tax_id_family <chr>, NCBI_tax_id_genus <chr>,
#> #   NCBI_tax_id_species <chr>, NCBI_tax_id_terminal <chr>
# }

refpath <- file.path(system.file("extdata",
                                 package = "parkinsonsMetagenomicData"),
                     "pathway_ref.parquet")

load_ref("pathway_ref", file_path = refpath)
#> # A tibble: 151 × 4
#>    pathway                          pathway_uniref pathway_genus pathway_species
#>    <chr>                            <chr>          <chr>         <chr>          
#>  1 3-HYDROXYPHENYLACETATE-DEGRADAT… 3-HYDROXYPHEN… NA            NA             
#>  2 3-HYDROXYPHENYLACETATE-DEGRADAT… 3-HYDROXYPHEN… g__Enterobac… s__Enterobacte…
#>  3 3-HYDROXYPHENYLACETATE-DEGRADAT… 3-HYDROXYPHEN… g__Escherich… s__Escherichia…
#>  4 3-HYDROXYPHENYLACETATE-DEGRADAT… 3-HYDROXYPHEN… g__Klebsiella s__Klebsiella_…
#>  5 3-HYDROXYPHENYLACETATE-DEGRADAT… 3-HYDROXYPHEN… g__Klebsiella s__Klebsiella_…
#>  6 3-HYDROXYPHENYLACETATE-DEGRADAT… 3-HYDROXYPHEN… g__Klebsiella s__Klebsiella_…
#>  7 AEROBACTINSYN-PWY: aerobactin b… AEROBACTINSYN… NA            NA             
#>  8 AEROBACTINSYN-PWY: aerobactin b… AEROBACTINSYN… g__Klebsiella s__Klebsiella_…
#>  9 ALLANTOINDEG-PWY: superpathway … ALLANTOINDEG-… NA            NA             
#> 10 ALLANTOINDEG-PWY: superpathway … ALLANTOINDEG-… g__Escherich… s__Escherichia…
#> # ℹ 141 more rows