loadRaw-methods {xcms} | R Documentation

## Read binary data from a source

### Description

This function extracts the raw data which will be used an `xcmsRaw` object. Further processing of data is done in the `xcmsRaw` constructor.

### Arguments

`object` | Specification of a data source (such as a file name or database query)

### Details

The implementing methods decide how to gather the data.

### Value

A list containing elements describing the data source. The `rt`, `scanindex`, `tic`, and `acquisitionNum` components each have one entry per scan. They are parallel in the sense that `rt[1]`, `scanindex[1]`, and `acquisitionNum[1]` all refer to the same scan. The list containst the following components:

``rt`` | Numeric vector with acquisition time (in seconds) for each scan
``tic`` | Numeric vector with Total Ion Count for each scan
``scanindex`` | Integer vector with starting positions of each scan in the `mz` and `intensity` components. It is an exclusive offset, so `scanindex[i]` is the offset in `mz` and `intensity` before the beginning of scan `i`. This means that the `mz` (respectively `intensity`) values for scan `i` would be from `scanindex[i] + 1` to `scanindex[i + 1]`
``mz`` | Concatenated vector of m/z values for all scans
``intensity`` | Concatenated vector of intensity values for all scans

### Methods

`signature(object = "xcmsSource")`

  Uses `loadRaw,xcmsSource-method` to extract raw data. Subclasses of `xcmsSource` can provide different ways of fetching data.

### Author(s)

Daniel Hackney, dan@haxney.org

### See Also

`xcmsRaw-class`, `xcmsSource`

[Package xcms version 3.9.1 Index]