grabMzxmlBPC: Grab the BPC or TIC from a file

In RaMS: R Access to Mass-Spec Data

Grab the BPC or TIC from a file

Description

The base peak intensity and total ion current are actually written into the mzXML files and aren't encoded, making retrieval of BPC and TIC information blazingly fast if parsed correctly.

Usage

grabMzxmlBPC(xml_data, TIC = FALSE, rtrange, incl_polarity)

Arguments

xml_data	An 'xml2' nodeset, usually created by applying 'read_xml' to an mzML file.
TIC	Boolean. If TRUE, the TIC is extracted rather than the BPC.
rtrange	A vector of length 2 containing an upper and lower bound on retention times of interest. Providing a range here can speed up load times (although not enormously, as the entire file must still be read) and reduce the final object's size.
incl_polarity	Boolean determining whether the polarity of the scan should be returned as a column in the table (positive mode = 1, negative mode = -1)

Value

A 'data.table' with columns for retention time (rt), and intensity (int).

RaMS documentation built on Oct. 9, 2024, 9:06 a.m.