MSmapMSmap-class.RdA 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 can be created with the MSmap constructor. The
constructor has the following arguments:
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.
A numeric of length 1 defining the lower bound
of the M/Z range of the MS map.
A numeric of length 1 defining the upper bound
of the M/Z range of the MS map.
The resolution along the M/Z range.
An optional data.frame as produced by
mzR::header(object). If missing, will be computer within
the function. Ignored when object is an
OnDiskMSnExp.
Set 0 intensities to NA. This can be used
to clarify the 3 dimensional plot produce by plot3D.
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.
signature(from = "MSmap", to = "data.frame"):
convert the MSmap instance in a data.frame. Useful
for plotting with lattice or ggplot2.
signature(object = "MSmap"): returns the raw
data filename.
signature(object = "MSmap"): returns the MS
level of the map spectra.
signature(object = "MSmap"): returns the actual
map matrix.
signature(object = "MSmap", ...): returns the M/Z values
of the map. Additional arguments are currently ignored.
signature(object = "MSmap", ...): returns retention
time values of the map. Additional arguments are currently ignored.
signature(object = "MSmap"): returns the
resolution with which the sample along the M/Z range was done.
signature(x = "MSmap"): returns the dimensions of
the map. ncol and nrow return the number of columns
and rows respectively.
signature(x = "MSmap"): transposes the map.
signature(object = "MSmap"): prints a summary of
the map.
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.
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.
if (FALSE) {
## 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)
}