convert: Convert raw files to mzML format
In jasenfinch/grover: Web API Framework for Mass Spectrometry Data Transfer

convertFile

R Documentation

Convert raw files to mzML format

Description

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

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

## S4 method for signature '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.