read_many_biotyper_reports: Importing a list of Bruker MALDI Biotyper CSV reports

In maldipickr: Dereplicate and Cherry-Pick Mass Spectrometry Spectra

Importing a list of Bruker MALDI Biotyper CSV reports

Description

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
)

maldipickr documentation built on Sept. 13, 2024, 1:12 a.m.