Parses skyline peak integration results into a tibble

Usage

parse_skyline_result(path, na_strings, silent = FALSE, ...)

Arguments

path: File name of the Skyline result file (*.tsv or *.csv)
na_strings: A character vector of strings to be interpreted as NA values.
silent: No comments printed
...: Additional arguments passed to the function. Currently only transition_id_columns, which is used for Skyline-like data files. The column mapped to feature_id will be appended with following info: if transition_id_columns = "name", the function will use the method_precursor_name and method_product_name columns to create unique feature IDs. If transition_id_columns = "mz", the function will use the method_precursor_mz and method_product_mz columns to create unique feature IDs.

Value

A tibble in the long format

Examples


file_path = system.file("extdata", "Skyline_MoleculeTransitionResults.csv", package = "mrmhub")

tbl <- parse_skyline_result(path = file_path, na_strings = "NA")

head(tbl)
#> # A tibble: 6 × 10
#>   analysis_id feature_id feature_class integration_qualifier method_precursor_mz
#>   <chr>       <chr>      <chr>         <lgl>                               <dbl>
#> 1 SBLK1       Aldostero… Steroids      FALSE                                359.
#> 2 SBLK1       Aldostero… Steroids      FALSE                                359.
#> 3 SBLK1       Aldostero… Steroids      FALSE                                361.
#> 4 SBLK1       Aldostero… Steroids      FALSE                                361.
#> 5 SBLK1       Aldostero… Steroids      FALSE                                363.
#> 6 SBLK1       Aldostero… Steroids      FALSE                                363.
#> # ℹ 5 more variables: method_precursor_name <chr>, method_product_mz <dbl>,
#> #   method_product_name <chr>, feature_rt <dbl>, feature_area <dbl>