isolationWindow-methods {mzR} | R Documentation

## Returns the ion selection isolation window

### Description

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.

### Methods

`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.

`signature(object = "mzRramp", unique. = "logical", simplify = "logical")`

  As above for `mzRramp` object.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk> based on the functionality from the `msPurity:::get_isolation_offsets` function.

### Examples

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

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

[Package mzR version 2.21.1 Index]