Convert raw files to mzML format — convertFile • grover

Convert a raw MS file using a grover API.

Usage

convertFile(
  grover_client,
  instrument,
  directory,
  file,
  args = "",
  outDir = ".",
  zip = TRUE,
  overwrite = FALSE
)

convertDirectory(
  grover_client,
  instrument,
  directory,
  args = "",
  outDir = ".",
  zip = TRUE,
  overwrite = FALSE,
  exclude = character()
)

convertDirectorySplitModes(
  grover_client,
  instrument,
  directory,
  args = "",
  outDir = ".",
  zip = TRUE
)

# S4 method for GroverClient
convertFile(
  grover_client,
  instrument,
  directory,
  file,
  args = NULL,
  outDir = ".",
  zip = TRUE,
  overwrite = FALSE
)

# S4 method for GroverClient
convertDirectory(
  grover_client,
  instrument,
  directory,
  args = "",
  outDir = ".",
  zip = TRUE,
  overwrite = FALSE,
  exclude = character()
)

# S4 method for GroverClient
convertDirectorySplitModes(
  grover_client,
  instrument,
  directory,
  args = "",
  outDir = ".",
  zip = TRUE
)

Arguments

grover_client: S4 object of class GroverClient
instrument: instrument name
directory: directory name
file: file name
args: arguments to pass to msconverteR::convert_files
outDir: output directory path for converted files
zip: zip converted file
overwrite: overwrite local mzML files that already exist at the outDir path that have the same file name as the raw files to be converted
exclude: A character vector of regular expression patterns for which raw files with matching patterns will not be converted.

Value

A vector of file paths to converted data files.