mutate_ms2: Mutate MS2 Data in mass_dataset Object

In tidymass/massdataset: massdataset

Mutate MS2 Data in mass_dataset Object

Description

This function adds MS2 data to a mass_dataset object. It reads MS2 files from a specified path, matches them with MS1 data in the object, and stores the matched MS2 data in the object.

Usage

mutate_ms2(
  object,
  column = c("rp", "hilic"),
  polarity = c("positive", "negative"),
  ms1.ms2.match.mz.tol = 15,
  ms1.ms2.match.rt.tol = 30,
  path = "."
)

Arguments

object	A mass_dataset object.
column	A character vector specifying the column types. Default is c("rp", "hilic").
polarity	A character vector specifying the polarity. Default is c("positive", "negative").
ms1.ms2.match.mz.tol	Numeric, the m/z tolerance for matching MS1 and MS2. Default is 15.
ms1.ms2.match.rt.tol	Numeric, the retention time tolerance for matching MS1 and MS2. Default is 30.
path	Character, the directory path where MS2 files are located. Default is the current directory.

Value

A modified mass_dataset object with added MS2 data.

Author(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
  data("expression_data")
  data("sample_info")
  data("variable_info")
  object =
    create_mass_dataset(
      expression_data = expression_data,
      sample_info = sample_info,
      variable_info = variable_info,
    )
  
  object
  
  dir.create("demo_data")
  system.file("ms2_data", package = "metid")
  file.copy(
    file.path(
      system.file("ms2_data", package = "massdataset"),
      "QC_MS2_NCE25_1.mgf"
    ),
    to = "demo_data",
    overwrite = TRUE
  )
  
  object =
    mutate_ms2(object = object,
               column = "rp",
               polarity = "positive")
  
  object@ms2_data

## End(Not run)

tidymass/massdataset documentation built on Sept. 14, 2024, 4:41 p.m.