get_run_code
get_run_code(
input_path = ".",
output_path,
msconvert_parameter,
docker_parameters = c(),
process_all = FALSE
)input path (raw data)
output path. If missing, same with input_path.
msconvert parameters. See
docker_parameters
process all raw data together or one by one.
Code can run in bash.
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
#> --------------------
#> pacakge_name: massconverter
#> function_name: create_msconvert_parameter
#> time: 2022-09-19 16:18:58
#> parameters:
#> 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
get_run_code(
input_path = "demo_data/raw_data",
output_path = "demo_data/mzxml",
msconvert_parameter = parameter,
process_all = FALSE
)
#> Warning: No raw data in /Users/xiaotaoshen/tidymass/massconverter/docs/reference/demo_data/raw_data
#> NULL