MSnbase: MSmap-class – R documentation

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MSmap-class

Class MSmap

Description

A class to store mass spectrometry data maps, i.e intensities collected along the M/Z and retention time space during a mass spectrometry acquisition.

Objects from the Class

Objects can be created with the MSmap constructor. The constructor has the following arguments:

object: An object created by mzR::openMSfile or an instance of class OnDiskMSnExp. If the latter contains data from multiple files, a warning will be issued and the first one will be used.
lowMz: A numeric of length 1 defining the lower bound of the M/Z range of the MS map.
highMz: A numeric of length 1 defining the upper bound of the M/Z range of the MS map.
resMz: The resolution along the M/Z range.
hd: An optional data.frame as produced by mzR::header(object). If missing, will be computer within the function. Ignored when object is an OnDiskMSnExp.
zeroIsNA: Set 0 intensities to NA. This can be used to clarify the 3 dimensional plot produce by plot3D.

Slots

call:: Object of class "call" - the call used to generate the instance.
map:: Object of class "matrix" containing the actual MS map.
mz:: Object of class "numeric" with the M/Z sampling bins.
res:: Object of class "numeric" storing the the M/Z resolution used to create the map.
rt:: Object of class "numeric" with the retention times of the map spectra.
ms:: Object of class "numeric" with the MS levels of the spectra.
t:: Object of class "logical" indicating if the instance has been transposed.
filename:: Object of class "character" specifying the filename of the original raw MS data.

Methods

coerce: signature(from = "MSmap", to = "data.frame"): convert the MSmap instance in a data.frame. Useful for plotting with lattice or ggplot2.
fileName: signature(object = "MSmap"): returns the raw data filename.
msLevel: signature(object = "MSmap"): returns the MS level of the map spectra.
msMap: signature(object = "MSmap"): returns the actual map matrix.
mz: signature(object = "MSmap", ...): returns the M/Z values of the map. Additional arguments are currently ignored.
rtime: signature(object = "MSmap", ...): returns retention time values of the map. Additional arguments are currently ignored.
mzRes: signature(object = "MSmap"): returns the resolution with which the sample along the M/Z range was done.
dim: signature(x = "MSmap"): returns the dimensions of the map. ncol and nrow return the number of columns and rows respectively.
t: signature(x = "MSmap"): transposes the map.
show: signature(object = "MSmap"): prints a summary of the map.
plot: signature(x = "MSmap", allTicks = "logical"): produces an image of the map using lattice::levelplot. By default, allTicks is TRUE and all M/Z and retention times ticks of drawn. If set to FALSE, only 10 ticks in each dimension are plotted.
plot3D: signature(object = "MSmap", rgl = "logical"): produces an three dimensional view of the map using lattice::cloude(..., type = "h"). If rgl is TRUE, the map is visualised on a rgl device and can be rotated with the mouse.

Author(s)

Laurent Gatto <lg390@cam.ac.uk>

Examples

## Not run: 
    ## downloads the data
    library("rpx")
    px1 <- PXDataset("PXD000001")
    (i <- grep("TMT.+mzML", pxfiles(px1), value = TRUE))
    mzf <- pxget(px1, i)

    ## Using an mzRpwiz object
    ## reads the data 
    ms <- openMSfile(mzf)
    hd <- header(ms)

    ## a set of spectra of interest: MS1 spectra eluted
    ## between 30 and 35 minutes retention time
    ms1 <- which(hd$msLevel == 1)
    rtsel <- hd$retentionTime[ms1] / 60 > 30 &
        hd$retentionTime[ms1] / 60 < 35

    ## the map
    M <- MSmap(ms, ms1[rtsel], 521, 523, .005, hd)

    plot(M, aspect = 1, allTicks = FALSE)
    plot3D(M)
    if (require("rgl") & interactive())
        plot3D(M, rgl = TRUE)

    ## With some MS2 spectra
    i <- ms1[which(rtsel)][1]
    j <- ms1[which(rtsel)][2]
    M2 <- MSmap(ms, i:j, 100, 1000, 1, hd)
    plot3D(M2)

    ## Using an OnDiskMSnExp object and accessors
    msn <- readMSData(mzf, mode = "onDisk")
    
    ## a set of spectra of interest: MS1 spectra eluted
    ## between 30 and 35 minutes retention time
    ms1 <- which(msLevel(msn) == 1)
    rtsel <- rtime(msn)[ms1] / 60 > 30 &
        rtime(msn)[ms1] / 60 < 35

    ## the map
    M3 <- MSmap(msn, ms1[rtsel], 521, 523, .005)
    plot(M3, aspect = 1, allTicks = FALSE)

    ## With some MS2 spectra
    i <- ms1[which(rtsel)][1]
    j <- ms1[which(rtsel)][2]
    M4 <- MSmap(msn, i:j, 100, 1000, 1)
    plot3D(M4)    

## End(Not run)

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release