omicsTools (version 1.1.7)

process_mrm_duplicates: Process All MRM Transitions for Duplicates

Description

This function takes a tibble containing MRM transition data, processes each sample_id separately to detect duplicates, and adds a column `MRM_Duplicate_Flag` indicating if a row is a duplicate based on the criteria: same polarity, less than a 1-minute retention time difference, and the same MRM transition (Q1/Q3).

Usage

process_mrm_duplicates(
  mrm_data,
  sample_name_col = "data_filename",
  sample_id_col = "sample_id",
  polarity_col = "polarity",
  retention_time_col = "retention_time",
  mass_info_col = "Mass Info",
  component_name_col = "component_name"
)

Value

The original tibble with an added `MRM_Duplicate_Flag` column.

Arguments

mrm_data

A tibble containing the MRM transition data.

sample_name_col

Name of the column containing sample name information.

sample_id_col

Name of the column containing sample ID information.

polarity_col

Name of the column containing polarity information.

retention_time_col

Name of the column containing retention time information.

mass_info_col

Name of the column containing mass information.

component_name_col

Name of the column containing component name information.

Author

Yaoxiang Li

Examples

if (FALSE) {
mrm_data <- tibble::tribble(
  ~`data_filename`, ~`sample_id`, ~polarity, ~`retention_time`, ~`Mass Info`, ~`component_name`,
  "Sample1", "ID1", "Positive", 1.95, "61.0 / 44.0", "Urea_pos",
  "Sample1", "ID1", "Positive", 8.34, "206.0 / 189.0", "Lipoamide_pos",
  "Sample2", "ID2", "Positive", 2.18, "339.1 / 110.0", "AICAR_pos",
  "Sample2", "ID2", "Positive", 1.76, "175.1 / 70.0", "Arginine_pos")
processed_data <- process_mrm_duplicates(
  mrm_data,
  "data_filename",
  "sample_id",
  "polarity",
  "retention_time",
  "Mass Info",
  "component_name"
)
print(processed_data)
}