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)