grabMzmlMS1: Extract the MS1 data from an mzML nodeset

In RaMS: R Access to Mass-Spec Data

Extract the MS1 data from an mzML nodeset

Description

Extract the MS1 data from an mzML nodeset

Usage

grabMzmlMS1(xml_data, rtrange, file_metadata, prefilter, incl_polarity)

Arguments

xml_data	An 'xml2' nodeset, usually created by applying 'read_xml' to an mzML file.
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.
file_metadata	Information about the file used to decode the binary arrays containing m/z and intensity information.
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.