create_msconvert_parameter: create_msconvert_parameter

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

create_msconvert_parameter

Description

Create msconvert parameters for convert_raw_data

Usage

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(s)

Xiaotao Shen [e-mail]

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

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