get_run_code: get_run_code

In tidymass/massconverter: Convert mass spectrometry raw data to othter format data

get_run_code

Description

get_run_code

Usage

get_run_code(
  input_path = ".",
  output_path,
  msconvert_parameter,
  docker_parameters = c(),
  process_all = FALSE
)

Arguments

input_path	input path (raw data)
output_path	output path. If missing, same with input_path.
msconvert_parameter	msconvert parameters. See
docker_parameters	docker_parameters
process_all	process all raw data together or one by one.

Value

Code can run in bash.

Author(s)

Xiaotao Shen [e-mail]

Examples

parameter =
  create_msconvert_parameter(
    output_format = "mzXML",
    binary_encoding_precision = "32",
    zlib = TRUE,
    write_index = TRUE,
    peak_picking_algorithm = "cwt",
    vendor_mslevels = c(1, NA),
    cwt_mslevels = c(1, NA),
    cwt_min_snr = 0.1,
    cwt_min_peak_spacing = 0.1,
    subset_polarity = "positive",
    subset_scan_number = c(NA, NA),
    subset_scan_time = c(60, 300),
    subset_mslevels = c(1, 2),
    zero_samples_mode = "removeExtra",
    zero_samples_mslevels = c(1, NA),
    zero_samples_add_missing_flanking_zero_count = 5
  )
parameter

get_run_code(
  input_path = "demo_data/raw_data",
  output_path = "demo_data/mzxml",
  msconvert_parameter = parameter,
  process_all = FALSE
)

tidymass/massconverter documentation built on Sept. 25, 2022, 1:53 p.m.