grabMzxmlMS1: Extract the MS1 data from an mzXML nodeset

In RaMS: R Access to Mass-Spec Data

Extract the MS1 data from an mzXML nodeset

Description

Extract the MS1 data from an mzXML nodeset

Usage

grabMzxmlMS1(xml_data, file_metadata, rtrange, prefilter, incl_polarity)

Arguments

xml_data	An 'xml2' nodeset, usually created by applying 'read_xml' to an mzXML file.
file_metadata	Information about the file used to decode the binary arrays containing m/z and intensity information.
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.
prefilter	The lowest intensity value of interest, used to reduce file size (and especially useful for profile mode data with many 0 values)
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), m/z (mz), and intensity (int).

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