Package 'grover'

Conversion arguments

Description

Helper functions for msconvert arguments for raw data conversion.

Usage

conversionArgsPeakPick()

conversionArgsNegativeMode()

conversionArgsPositiveMode()

conversionArgsMSlevel1()

conversionArgsMSlevel2()

conversionArgsMSlevel3()

Details

These functions return character strings suitable for supplying to the args argument of convertFile for passing to msconvert.

Examples

conversionArgsPeakPick()

---

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.

Value

A vector of file paths to converted data files.

---

Check the existance of a grover API

Description

Check grover API is still extistant.

Usage

extant(grover_client)

## S4 method for signature 'GroverClient'
extant(grover_client)

Arguments

grover_client

S4 object of class GroverGlient

Value

TRUE if the API host is accessible and FALSE if not.

---

Retrieve file information

Description

Return file information for a given file using the grover API.

Usage

fileInfo(grover_client, instrument, directory, file)

directoryFileInfo(grover_client, instrument, directory)

instrumentFileInfo(grover_client, instrument)

repositoryFileInfo(grover_client)

## S4 method for signature 'GroverClient'
fileInfo(grover_client, instrument, directory, file)

## S4 method for signature 'GroverClient'
directoryFileInfo(grover_client, instrument, directory)

## S4 method for signature 'GroverClient'
instrumentFileInfo(grover_client, instrument)

## S4 method for signature 'GroverClient'
repositoryFileInfo(grover_client)

Arguments

grover_client	S4 object of class GroverClient
instrument	instrument name
directory	directory name
file	file name

---

GroverClient and GroverHost class constructor

Description

Create a GroverClient or GroverHost class object containing API host information.

Usage

grover(host, port, auth, repository = NULL)

Arguments

host	host address
port	port on which the API is hosted
auth	authentication key
repository	data repository directory path

Examples

## Grover client 
grover_client <- grover(host = "127.0.0.1",
                     port = 8000,
                     auth = "1234")

## Grover host
grover_host <- grover(host = "127.0.0.1",
                     port = 8000,
                     auth = "1234",
                     repository = system.file('repository',
                                               package = 'grover'))

---

Grover API

Description

Run the grover REST API for file conversion.

Usage

groverAPI(
  grover_host,
  background = FALSE,
  log_dir = "~/.grover/logs",
  temp_dir = tempdir()
)

Arguments

grover_host	S4 object of class Grover
background	Run as a background process.
log_dir	directory path for API logs
temp_dir	temporary directory for converted files

Examples

## Not run: 
grover_host <- grover(host = "127.0.0.1",
                     port = 8000,
                     auth = "1234",
                     repository = system.file('repository',
                                               package = 'grover'))
groverAPI(grover_host) 

## End(Not run)

---

GroverClient class

Description

A simple S4 class containing grover API host information for client-side use.

Slots

host

host address

port

port on which the API is hosted

auth

authentication key

---

GroverHost class

Description

A simple S4 class containing host information for configuring a grover API.

Details

This class inherits from the GroverClient class so GroverClient accessor methods are applicable.

Slots

host

host address

port

port on which the API is hosted

auth

authentication key

repository

directory path to the raw mass spectrometry data repository

---

GroverClient get and set methods

Description

Retrieve or set host information for a GroverClient objects.

Usage

host(grover_client)

host(grover_client) <- value

port(grover_client)

port(grover_client) <- value

auth(grover_client)

auth(grover_client) <- value

## S4 method for signature 'GroverClient'
host(grover_client)

## S4 replacement method for signature 'GroverClient'
host(grover_client) <- value

## S4 method for signature 'GroverClient'
port(grover_client)

## S4 replacement method for signature 'GroverClient'
port(grover_client) <- value

## S4 method for signature 'GroverClient'
auth(grover_client)

## S4 replacement method for signature 'GroverClient'
auth(grover_client) <- value

Arguments

grover_client	S4 object of class GroverClient
value	new host value to set

---

List raw data repository contents

Description

List available instruments, experiment directories or samples using a grover API.

Usage

listInstruments(grover_client)

listDirectories(grover_client, instrument)

listFiles(grover_client, instrument, directory)

listRawFiles(grover_client, instrument, directory)

## S4 method for signature 'GroverClient'
listInstruments(grover_client)

## S4 method for signature 'GroverClient'
listDirectories(grover_client, instrument)

## S4 method for signature 'GroverClient'
listFiles(grover_client, instrument, directory)

## S4 method for signature 'GroverClient'
listRawFiles(grover_client, instrument, directory)

Arguments

grover_client	S4 object of class GroverClient
instrument	instrument name
directory	directory name

---

Parse a grover configuration file

Description

Read grover API host information from a text file.

Usage

readGrover(path = "grover.yml")

Arguments

path	file path to text file containing host information

Details

The text file should contain 3 lines, the first the host address, the second the port on which it is hosted and lastly the authentication key needed

Examples

## Grover client
grover_client <- system.file('grover_client.yml',
                              package = 'grover')
grover_client <- readGrover(grover_client)

## Grover host
grover_host <- system.file('grover_host.yml',
                              package = 'grover')
grover_host <- readGrover(grover_host)

---

GroverHost get and set methods

Description

Retrieve or set host information for GroverHost objects.

Usage

repository(grover_host)

repository(grover_host) <- value

## S4 method for signature 'GroverHost'
repository(grover_host)

## S4 replacement method for signature 'GroverHost'
repository(grover_host) <- value

Arguments

grover_host	S4 object of class GroverHost
value	new host value to set

---

Retrieve sample raw file header information

Description

Get sample header information for a given raw file or directory using a grover API.

Usage

sampleInfo(grover_client, instrument, directory, file)

runInfo(grover_client, instrument, directory, exclude = character())

## S4 method for signature 'GroverClient'
sampleInfo(grover_client, instrument, directory, file)

## S4 method for signature 'GroverClient'
runInfo(grover_client, instrument, directory, exclude = character())

Arguments

grover_client	S4 object of class GroverClient
instrument	instrument name
directory	directory name
file	file name
exclude	A character vector of regular expression patterns for which the information matching files will not be retrieved.

---

Grover class show methods

Description

Show method for class S4 Grover.

Usage

## S4 method for signature 'GroverClient'
show(object)

## S4 method for signature 'GroverHost'
show(object)

Arguments

object

S4 object of class Grover

---

Transfer files

Description

Transfer a file or directory using a grover API.

Usage

transferFile(grover_client, instrument, directory, file, outDir = ".")

transferDirectory(grover_client, instrument, directory, outDir = ".")

## S4 method for signature 'GroverClient'
transferFile(grover_client, instrument, directory, file, outDir = ".")

## S4 method for signature 'GroverClient'
transferDirectory(grover_client, instrument, directory, outDir = ".")

Arguments

grover_client	S4 object of class GroverClient
instrument	instrument name
directory	directory name
file	file name
outDir	output directory path for transferred file

---

Return the version of a grover API

Description

Return the version number of a grover API.

Usage

version(grover_client)

## S4 method for signature 'GroverClient'
version(grover_client)

Arguments

grover_client

S4 object of class GroverGlient

Value

The version number of the grover API.

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