extractMsData,OnDiskMSnExp-method {xcms} | R Documentation

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

### Description

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. `plotMsData` to plot the data for a single file.

### Examples

    ## Read some files from the test data package.
    library(faahKO)
    library(xcms)
    fls <- dir(system.file("cdf/KO", package = "faahKO"), recursive = TRUE,
               full.names = TRUE)
    raw_data <- readMSData(fls[1:2], mode = "onDisk")

    ## Read the full MS data for a defined mz-rt region.
    res <- extractMsData(raw_data, mz = c(300, 320), rt = c(2700, 2900))

    ## We've got one data.frame per file
    length(res)

    ## With number of rows:
    nrow(res[[1]])

    head(res[[1]])

[Package xcms version 3.0.2 Index]