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Importing a list of Bruker MALDI Biotyper CSV reports

Source: R/read_many_biotyper_reports.R
read_many_biotyper_reports.Rd

Importing a list of Bruker MALDI Biotyper CSV reports

Usage

read_many_biotyper_reports(path_to_reports, report_ids, best_hits = TRUE, ...)

Arguments

path_to_reports

A vector of paths to the csv files to be imported by read_biotyper_report().

report_ids

A vector of character names for each of the reports.

best_hits

A logical indicating whether to return only the best hit in the read_biotyper_report() function.

...

Name-value pairs to be passed on to dplyr::mutate()

Value

A tibble just like the one returned by the read_biotyper_report() function, except that the name of the spot of the MALDI target (i.e., plate) is registered to the original_name column (instead of the name column), and the column name consist in the provided report_ids used as a prefix of the original_name column.

Note

The report identifiers are sanitized to convert all dashes (-) as underscores (_).

See also

read_biotyper_report

Examples

# List of Bruker MALDI Biotyper reports
reports_paths <- system.file(
  c("biotyper.csv", "biotyper.csv", "biotyper.csv"),
  package = "maldipickr"
)
# Read the list of reports and combine them in a single tibble
read_many_biotyper_reports(
  reports_paths,
  report_ids = c("first", "second", "third"),
  # Additional metadata below are passed to dplyr::mutate
  growth_temperature = 37.0
)
#> # A tibble: 9 × 10
#>   name          original_name sample_name hit_rank bruker_quality bruker_species
#>   <chr>         <chr>         <chr>          <int> <chr>          <chr>         
#> 1 first_targetA targetA       NA                 1 -              not reliable …
#> 2 first_targetB targetB       NA                 1 +++            Escherichia c…
#> 3 first_targetC targetC       NA                 1 +++            Kosakonia cow…
#> 4 second_targe… targetA       NA                 1 -              not reliable …
#> 5 second_targe… targetB       NA                 1 +++            Escherichia c…
#> 6 second_targe… targetC       NA                 1 +++            Kosakonia cow…
#> 7 third_targetA targetA       NA                 1 -              not reliable …
#> 8 third_targetB targetB       NA                 1 +++            Escherichia c…
#> 9 third_targetC targetC       NA                 1 +++            Kosakonia cow…
#> # ℹ 4 more variables: bruker_taxid <dbl>, bruker_hash <chr>, bruker_log <dbl>,
#> #   growth_temperature <dbl>