generate_process_report: Generate Process Report for Sciex 7500/5500 Raw Data

Description

This function generates a comprehensive process report for Sciex 7500/5500 raw data, including data normalization, missing value imputation, and optional normalization and flagging steps. The results are saved in a temporary directory and then zipped into a file for easy sharing.

Usage

generate_process_report(
  input_file,
  output_file = NULL,
  filter_blank = TRUE,
  blank_string = "Blank|BLANK|blank",
  filter_nist = TRUE,
  nist_string = "NIST|Nist|nist",
  imputation_threshold = 0.25,
  imputation_method = "half_min",
  qc_string = "QC",
  include_is_normalization = TRUE,
  include_qc_rlsc = TRUE,
  include_pqn = TRUE,
  include_qc_rsd = TRUE,
  include_snr_flag = TRUE,
  snr_threshold = 10,
  include_area_flag = TRUE,
  include_height_flag = TRUE,
  id_col = "sample_id",
  ignore_na = TRUE
)

Value

The path to the generated zip file containing the process report.

Arguments

input_file: The path to the input file containing raw data.
output_file: The path to the output zip file.
filter_blank: Logical, whether to filter out blank samples (default: TRUE).
blank_string: Character, regular expression pattern to match blank sample IDs (default: 'Blank|BLANK|blank').
filter_nist: Logical, whether to filter out NIST samples (default: TRUE).
nist_string: Character, regular expression pattern to match NIST sample IDs (default: 'NIST|Nist|nist').
imputation_threshold: Numeric, threshold for missing value imputation (default: 0.25).
imputation_method: Character, method for missing value imputation (default: 'half_min').
qc_string: Character, regular expression pattern to match QC sample IDs (default: 'QC').
include_is_normalization: Logical, whether to include internal standard normalization (default: TRUE).
include_qc_rlsc: Logical, whether to include QC-RLSC normalization (default: TRUE).
include_pqn: Logical, whether to include PQN normalization (default: TRUE).
include_qc_rsd: Logical, whether to include QC RSD calculation (default: TRUE).
include_snr_flag: Logical, whether to include Signal-to-Noise ratio flagging (default: TRUE).
snr_threshold: Numeric, threshold for Signal-to-Noise ratio flagging (default: 10).
include_area_flag: Logical, whether to include area threshold flagging (default: TRUE).
include_height_flag: Logical, whether to include height threshold flagging (default: TRUE).
id_col: Character, name of the column containing sample IDs (default: 'sample_id').
ignore_na: Logical, whether to ignore NA values in QC RSD calculation (default: TRUE).

Author

Yaoxiang Li