isolationWindow-methods: Returns the ion selection isolation window

isolationWindow-methodsR Documentation

Returns the ion selection isolation window


The methods return matrices of lower (column low) and upper (column high) isolation window offsets. Matrices are returned as a list of length equal to the number of input files (provided as file names of raw mass spectrometry data objects, see below). By default (i.e when unique. = TRUE ), only unique offsets are returned, as they are expected to identical for all spectra per acquisition. If this is not the case, a message is displayed.


signature(object = "character", unique. = "logical", simplify = "logical")

Returns the isolation window for the file object. By default, only unique isolation windows are returned per file (unique = TRUE); if set to FALSE, a matrix with as many rows as there are MS2 spectra. If only one file passed an input and simplify is set to TRUE (default), the resulting list of length 1 is simplified to a matrix.

signature(object = "mzRpwiz", unique. = "logical", simplify = "logical")

As above for mzRpwiz objects.


Laurent Gatto <> based on the functionality from the msPurity:::get_isolation_offsets function.


f <- msdata::proteomics(full.names = TRUE,
                        pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

rw <- openMSfile(f)
str(isolationWindow(rw, unique = FALSE))

sneumann/mzR documentation built on June 13, 2022, 3:10 p.m.