extractMsData,OnDiskMSnExp-method {xcms} | R Documentation

## DEPRECATED: Extract a `data.frame` containing MS data

### Description

UPDATE: the `extractMsData` and `plotMsData` functions are deprecated and `as(x, "data.frame")` and `plot(x, type = "XIC")` (`x` being an `OnDiskMSnExp` or `XCMSnExp` object) should be used instead. See examples below. Be aware that filtering the raw object might however drop the adjusted retention times. In such cases it is advisable to use the `applyAdjustedRtime()` function prior to filtering.

Extract a `data.frame` of retention time, mz and intensity values from each file/sample in the provided rt-mz range (or for the full data range if `rt` and `mz` are not defined).

### Usage

    ## S4 method for signature 'OnDiskMSnExp'
    extractMsData(object, rt, mz, msLevel = 1L)

    ## S4 method for signature 'XCMSnExp'
    extractMsData(
      object,
      rt,
      mz,
      msLevel = 1L,
      adjustedRtime = hasAdjustedRtime(object)
    )

### Arguments

`object` | A `XCMSnExp` or `OnDiskMSnExp` object.
`rt` | `numeric(2)` with the retention time range from which the data should be extracted.
`mz` | `numeric(2)` with the mz range.
`msLevel` | `integer` defining the MS level(s) to which the data should be sub-setted prior to extraction; defaults to `msLevel = 1L`.
`adjustedRtime` | (for `extractMsData,XCMSnExp`): `logical(1)` specifying if adjusted or raw retention times should be reported. Defaults to adjusted retention times, if these are present in `object`.

### Value

A `list` of length equal to the number of samples/files in `object`. Each element being a `data.frame` with columns `"rt"`, `"mz"` and `"i"` with the retention time, mz and intensity tuples of a file. If no data is available for the mz-rt range in a file a `data.frame` with 0 rows is returned for that file.

### Author(s)

Johannes Rainer

### See Also

`XCMSnExp` for the data object.

### Examples

    ## Read some files from the test data package.
    library(faahKO)
    library(xcms)
    library(magrittr)
    fls <- dir(system.file("cdf/KO", package = "faahKO"), recursive = TRUE,
               full.names = TRUE)
    raw_data <- readMSData(fls[1], mode = "onDisk")

    ## Disabling parallel processing for this example
    register(SerialParam())

    ## Extract the full data as a data.frame
    ms_all <- as(raw_data, "data.frame")
    head(ms_all)
    nrow(ms_all)

    ## Read the full MS data for a defined mz-rt region.
    res <- raw_data %>%
        filterRt(rt = c(2700, 2900)) %>%
        filterMz(mz = c(300, 320)) %>%
        as("data.frame")

    head(res)
    nrow(res)

[Package xcms version 3.10.2 Index]