| msSet {msProcess} | R Documentation |
An object of class msSet is a list containing three required components:
mz.
The number of columns should be the same as the length of type.
It can also have additional elements such as
"noise", "noise.local", "baseline", "tic",
"peak.list", "peak.class", "peak.matrix",
"intensity.mean", "noise.mean", and "noise.local.mean".
msSet(x, mz=NULL, type=NULL, data.name=NULL, ...)
x |
a vector, a matrix, a data.frame, or an object of class msSet. |
... |
additional elements to be added. |
data.name |
a character string denoting the name for the dataset.
Default: NULL, i.e., using the variable name of the x argument. |
mz |
a vector of m/z values. It must be of the same length as x if x is a vector,
or its length must be the same as the number of rows of x
if x is a matrix or data.frame. |
type |
a factor denoting the disease label for each spectrum.
This argument must be a scalar (length=1) if x is a vector,
or a vector whose length is the same as the number of rows of x
in the case that x is a matrix or data.frame. |
an object of class msSet.
msSet object.
Usage: x[i, j]
msSet object.Usage: image(x, what="spectra", subset=NULL, xaxis="mass", xlim=NULL, add=FALSE, xaxs="i", yaxs="i", ...)
msSet object."spectra", "noise", "noise.local",
"baseline", "peak.list", and "peak.matrix".
Default: "spectra".
If what=="peak.matrix",
the arguments subset, xaxis, and xlim are ignored."mass" and "time".
Default: "time".NULL (by default), the entire range of the data is plotted.
If one of its element is NA, it is replaced with the corresponding limit.TRUE, the plot is added using the current
par() layout. Otherwise a new plot is produced. Default: FALSE.par for details.par for details.image function.Usage: plot(x, process="msPrepare", subset=1, offset=0, xaxis="mass", xlim=NULL, pch=1, lty=1:2, col=1:8, lwd=1, add=FALSE, ...)
msSet object."msPrepare", "msDenoise",
"msNoise", "msDetrend",
"msNormalize", "msPeak",
"msAlign". Default: "msPrepare".NULL indicating the index of the
spectra to be plotted. Default: 1, i.e., the first spectrum.
If NULL, the entire set of spectra are plotted.NULL, the offset is automatically calculated.
Default: NULL."mass" and "time".
Default: "time".NULL (by default), the entire range of the data is plotted.
If one of its element is NA, it is replaced with the corresponding limit.TRUE, the plot is added using the current
par() layout. Otherwise a new plot is produced. Default: FALSE.msSet object.
Usage: print(x, justify="left", sep=":", ...) or x
msSet object."none", "left", "right" and "decimal".
Only the first letter needs to be given.msSet object.
Usage: summary(x)
msSet object.
if (!exists("qcset")) data("qcset", package="msProcess")
## plot a few spectra from qcset
plot(qcset, subset=1:5)
## image of all spectra in qcset
image(qcset)