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Importing Bruker MALDI Biotyper CSV report

Source: R/read_biotyper_report.R
read_biotyper_report.Rd

The header-less table exported by the Compass software in the Bruker MALDI Biotyper device is separated by semi-colons and has empty columns which prevent an easy import in R. This function reads the report correctly as a tibble.

Usage

read_biotyper_report(path, best_hits = TRUE, long_format = TRUE)

Arguments

path

Path to the semi-colon separated table

best_hits

A logical indicating whether to return only the best hits for each target analyzed

long_format

A logical indicating whether the table is in the long format (many rows) or wide format (many columns) when showing all the hits. This option has no effect when best_hits = TRUE.

Value

A tibble of 7 columns (best_hits = TRUE) or 52 columns (best_hits = FALSE). See Details for the description of the columns.

Details

The header-less table contains identification information for each target processed by the Biotyper device and once processed by the read_biotyper_report, the following seven columns are available in the tibble, when using the best_hits = TRUE option:

  • name: a character indicating the name of the spot of the MALDI target (i.e., plate)

  • sample_name: the character string provided during the preparation of the MALDI target (i.e., plate)

  • hit_rank: an integer indicating the rank of the hit for the corresponding target and identification

  • bruker_quality: a character encoding the quality of the identification with potentially multiple "+" symbol or only one "-"

  • bruker_species: the species name associated with the MALDI spectrum analyzed.

  • bruker_taxid: the NCBI Taxonomy Identifier of the species name in the column species

  • bruker_hash: a hash from an undocumented checksum function probably to encode the database entry.

  • bruker_log: the log-score of the identification.

When all hits are returned (with best_hits = FALSE), the default output format is the long format (long_format = TRUE), meaning that the previous columns remain unchanged, but all hits are now returned, thus increasing the number of rows.

When all hits are returned (with best_hits = FALSE) using the wide format (long_format = FALSE), the two columns nameandsample_nameremains unchanged, but the five columns prefixed bybruker_` contain the hit rank, creating a tibble of 52 columns:

  • bruker_01_quality

  • bruker_01_species

  • bruker_01_taxid

  • bruker_01_hash

  • bruker_01_log

  • bruker_02_quality

  • ...

  • bruker_10_species

  • bruker_10_taxid

  • bruker_10_hash

  • bruker_10_log

Note

A report that contains only spectra with no peaks found will return a tibble of 0 rows and a warning message.

See also

read_many_biotyper_reports

Examples

# Get a example Bruker report
biotyper <- system.file("biotyper.csv", package = "maldipickr")
# Import the report as a tibble
report_tibble <- read_biotyper_report(biotyper)
# Display the tibble
report_tibble
#> # A tibble: 3 × 8
#>   name    sample_name hit_rank bruker_quality bruker_species        bruker_taxid
#>   <chr>   <chr>          <int> <chr>          <chr>                        <dbl>
#> 1 targetA NA                 1 -              not reliable identif…           NA
#> 2 targetB NA                 1 +++            Escherichia coli               562
#> 3 targetC NA                 1 +++            Kosakonia cowanii           208223
#> # ℹ 2 more variables: bruker_hash <chr>, bruker_log <dbl>