MS Data Analysis

Description Arguments Details Value Methods Author(s) See Also

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

object

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

The implementing methods decide how to gather the data.

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 he 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

signature(object = "xcmsSource"): Uses loadRaw,xcmsSource-method to extract raw data. Subclasses of xcmsSource can provide different ways of fetching data.

Daniel Hackney, dan@haxney.org

xcmsRaw-class, xcmsSource

benjiec/xcms documentation built on May 12, 2019, 11:57 a.m.