create_msconvert_parameter

Create msconvert parameters for convert_raw_data

create_msconvert_parameter(
  output_format = c("mzXML", "mzML", "mz5", "mgf", "text", "ms1", "cms1", "ms2",
    "cms2"),
  binary_encoding_precision = c("64", "32"),
  zlib = TRUE,
  write_index = TRUE,
  peak_picking_algorithm = c("vendor", "cwt", "no"),
  vendor_mslevels = c(1, NA),
  cwt_mslevels = c(1, NA),
  cwt_min_snr = 0.1,
  cwt_min_peak_spacing = 0.1,
  subset_polarity = c("any", "positive", "negative"),
  subset_scan_number = c(NA, NA),
  subset_scan_time = c(NA, NA),
  subset_mslevels = c(1, NA),
  zero_samples_mode = c("no", "removeExtra", "addMissing"),
  zero_samples_mslevels = c(1, NA),
  zero_samples_add_missing_flanking_zero_count = 5
)

Arguments

output_format

"mzXML","mzML", "mz5", "mgf", "text", "ms1", "cms1", "ms2", or "cms2".

binary_encoding_precision

"64" or "32"

zlib

TRUE or not.

write_index

TRUE or not.

peak_picking_algorithm

"vendor" or "cwt"

vendor_mslevels

A two numeric vector. Second can be set as NA.

cwt_mslevels

A two numeric vector. Second can be set as NA.

cwt_min_snr

minimum signal-to-noise ratio

cwt_min_peak_spacing

minimum peak spacing

subset_polarity

"any", "positive" or "negative"

subset_scan_number

A two numeric vector. Can be c(NA, NA) if don't use this.

subset_scan_time

A two numeric vector. Can be c(NA, NA) if don't use this.

subset_mslevels

A two numeric vector. Second can be set as NA.

zero_samples_mode

"no", "removeExtra", or "addMissing".

zero_samples_mslevels

A two numeric vector. Second can be set as NA.

zero_samples_add_missing_flanking_zero_count

= 5

Value

error or code list

Author

Xiaotao Shen shenxt1990@outlook.com

Examples

parameter =
create_msconvert_parameter(
  output_format = "mzXML",
  binary_encoding_precision = "64",
  zlib = TRUE,
  write_index = TRUE,
  peak_picking_algorithm = "vendor",
  vendor_mslevels = c(1, 2),
  cwt_mslevels = c(1, NA),
  cwt_min_snr = 0.1,
  cwt_min_peak_spacing = 0.1,
  subset_polarity = "any",
  subset_scan_number = c(NA, NA),
  subset_scan_time = c(NA, NA),
  subset_mslevels = c(1, NA),
  zero_samples_mode = "no",
  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 16:18:57 
#> parameters:
#> output_format : mzXML 
#> binary_encoding_precision : 64 
#> zlib : TRUE 
#> write_index : TRUE 
#> peak_picking_algorithm : vendor 
#> vendor_mslevels : c(1, 2) 
#> cwt_mslevels : c(1, NA) 
#> cwt_min_snr : 0.1 
#> cwt_min_peak_spacing : 0.1 
#> subset_polarity : any 
#> subset_scan_number : c(NA, NA) 
#> subset_scan_time : c(NA, NA) 
#> subset_mslevels : c(1, NA) 
#> zero_samples_mode : no 
#> zero_samples_mslevels : c(1, NA) 
#> zero_samples_add_missing_flanking_zero_count : 5