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Parses a plain long CSV file

Source: R/data-import.R
parse_plain_long_csv.Rd

Parses a CSV table with analysis/samples and feature pairs in rows, columns representing the feature variables.

Usage

parse_plain_long_csv(
  path,
  na_strings = "NA",
  silent = FALSE,
  column_mapping = NULL,
  warn_unrecognized_columns = TRUE,
  ...
)

Arguments

path

File name (*.tsv or *.csv)

na_strings

A character vector of strings to be interpreted as NA values. Blank fields are also considered to be missing values.

silent

No comments printed

column_mapping

A named character vector with the mapping of the columns in the input file to the columns in the output table. If NULL (default), the function will use the default mapping. See import_data_csv_long() for details.

warn_unrecognized_columns

Logical indicating whether to issue a warning for unknown columns in the dataset.

...

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", "plain_long_dataset.csv", package = "midar")

tbl <- parse_plain_long_csv(path = file_path)
#> ! Following unrecognized columns present in the data and were ignored: "internal_standard", "batch", "sample_type", "rt_apex", "area_normalized", "concentration", "rt_int_start", and "rt_int_end".
#> ! Use argument `column_mapping` to define column mapping.

head(tbl)
#> # A tibble: 6 × 12
#>   analysis_id      raw_data_filename     acquisition_time_stamp feature_id      
#>   <chr>            <chr>                 <dttm>                 <chr>           
#> 1 Longit_batch1_15 Longit_batch1_15.mzML 2017-10-20 20:07:09    CE 18:1         
#> 2 Longit_batch1_16 Longit_batch1_16.mzML 2017-10-20 20:29:49    CE 18:1         
#> 3 Longit_batch1_17 Longit_batch1_17.mzML 2017-10-20 20:41:10    CE 18:1         
#> 4 Longit_batch1_15 Longit_batch1_15.mzML 2017-10-20 20:07:09    CE 18:1 d7 (IST…
#> 5 Longit_batch1_16 Longit_batch1_16.mzML 2017-10-20 20:29:49    CE 18:1 d7 (IST…
#> 6 Longit_batch1_17 Longit_batch1_17.mzML 2017-10-20 20:41:10    CE 18:1 d7 (IST…
#> # ℹ 8 more variables: integration_qualifier <lgl>, method_precursor_mz <dbl>,
#> #   method_product_mz <dbl>, method_collision_energy <dbl>,
#> #   method_polarity <chr>, feature_area <dbl>, feature_height <dbl>,
#> #   feature_fwhm <dbl>