Read binary data from a source

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

Methods

signature(object = "xcmsSource")

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

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

Author

Daniel Hackney, dan@haxney.org

See also

xcmsRaw-class, xcmsSource