getMSnRaw: Get MSn raw data

In iontree: Data management and analysis of ion trees from ion-trap mass spectrometry

Description

query MSn data by the attribute of 'msLevel' and get MSn raw data into a R list. Users may just use function "saveMSnRaw" to retrieve ion tree from a data file and avoid a direct Java function call.

Usage

getMSnRaw(msdata, msLevel = 2)

Arguments

msdata	msdata is a reference to a Java ArrayList. Obtained by calling getMSData Java function. msdata=.jcall("XCMS", "Ljava/util/ArrayList;","getMSData", filename);
msLevel	msLevel in integer

Value

premz	ancestral precursor ions
rt	retention time
msn.sp	a list of spectrum (m/z, intensity)

Note

MS1 data could be queried by msLevel=1. The return type is still a list but different components (rt, tic, sp).

Author(s)

Mingshu Cao

iontree documentation built on May 2, 2018, 2:55 a.m.