MSmap-class {MSnbase} | R Documentation

## 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)

[Package MSnbase version 2.12.0 Index]