omicsTools (version 1.1.7)

load_parse_sciex_txt: Load and Parse SCIEX OS Exported LC-MRM-MS2 Data

Description

Load and Parse SCIEX OS Exported LC-MRM-MS2 Data

Usage

load_parse_sciex_txt(
  file_path,
  input_data = NULL,
  return_all_columns = TRUE,
  check_negative_values = TRUE,
  fix_istds = TRUE
)

Value

tibble with the fields appropriately renamed.

Arguments

file_path

File path of the input text file of a complete output of the SCIEX OS results from a sequence. File should be tab-delimited and in the 'long' format.

input_data

Input tibble of raw SCIEX (pre-parsing) text file. If `NULL` (default value), data will be loaded from `file_path`.

return_all_columns

Logical value as to whether to return all columns (`TRUE`) or just the necessary columns for downstream machine learning analysis or quality control review (`FALSE`). Default value is `TRUE`. When set to false, the columns included in the returned tibble include: `"component_name"`, `"component_idx"`, `"precursor_mz"`, `"product_mz"`, `"is_istd"`, `"istd"`, `"retention_time_expected"`, `"data_filename"`, `"data_file_idx"`, `"sample_id"`, `"sample_type"`, `"component_type"`, `"polarity"`, `"component_group"`, `"outlier_reasons"`, `"retention_time_expected_istd"`, `"area"`, `"istd_area"`, `"area_ratio"`, `"height"`, `"istd_height"`, `"height_ratio"`, `"peak_quality"`, `"istd_peak_quality"`, `"retention_time"`, `"retention_time_istd"`, `"rt_error"`, `"rt_delta_min"`, `"rt_start"`, `"istd_rt_start"`, `"rt_end"`, `"istd_rt_end"`, `"peak_width"`, `"istd_peak_width"`, `"fwhm"`, `"istd_fwhm"`, `"signal_noise"`, `"istd_signal_noise"`, `"modified"`, `"relative_rt"`, `"used"`, `"tailing_factor"`, `"asymmetry_factor"`, `points_across_baseline"`, `"points_across_fwhm"`).

check_negative_values

Logical value as to whether to check for negative values in the `area` and `height` variables (for both components and internal standards). If `TRUE` (default) and there is at least one negative value in the data, the minimum `area` or `height` value will be subtracted from all `area` and/or `height` values by `component_name`, and 100 will then be added to avoid having values below 100. `area_ratio`, `height_ratio`, and `area_height_ratio` values (and their internal standard equivalent variables) will also be re-calculated.

fix_istds

Logical value (default `TRUE`) to identify internal standards by regular expression of "(\.IS$)|(_IS$)|(_d[0-9]+_)|(\(d[0-9]+\))".

Author

Yaoxiang Li

Examples

if (FALSE) {
data(sciex_mrm_ms_data)
data_tibble <- load_parse_sciex_txt(
  file_path = "path/to/file.txt",
  return_all_columns = FALSE,
  check_negative_values = TRUE
)
}