isolationWindow-methods: Returns the ion selection isolation window

In mzR: parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

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 <[e-mail]> 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))

Example output

Loading required package: Rcpp
Loading required namespace: XML
     low high
[1,]   1    1
     low high
[1,]   1    1
 num [1:451, 1:2] 1 1 1 1 1 1 1 1 1 1 ...
 - attr(*, "dimnames")=List of 2
  ..$ : NULL
  ..$ : chr [1:2] "low" "high"

mzR documentation built on Nov. 20, 2020, 2 a.m.