Description Usage Arguments Details Value Note Author(s) See Also Examples
The profile matrix is an n x m matrix, n (rows) representing equally spaced m/z values (bins) and m (columns) the retention time of the corresponding scans. Each cell contains the maximum intensity measured for the specific scan and m/z values falling within the m/z bin.
The profMat
method creates a new profile matrix or returns the
profile matrix within the object's @env
slot, if available.
Settings for the profile matrix generation, such as step
(the bin
size), method
or additional settings are extracted from the
respective slots of the xcmsRaw
object.
Alternatively it is possible to specify all of the settings as
additional parameters.
1 2 |
object |
The |
method |
The profile matrix generation method. Allowed are |
step |
numeric(1) representing the m/z bin size. |
baselevel |
numeric(1) representing the base value to which
empty elements (i.e. m/z bins without a measured intensity) should be
set. Only considered if |
basespace |
numeric(1) representing the m/z length after
which the signal will drop to the base level. Linear interpolation will
be used between consecutive data points falling within
|
mzrange. |
Optional numeric(2) manually specifying the mz value range to be used for binnind. If not provided, the whole mz value range is used. |
Profile matrix generation methods:
The default profile matrix generation method that does a simple binning, i.e. aggregating of intensity values falling within an m/z bin.
Binning followed by linear interpolation to impute missing values. The value for m/z bins without a measured intensity are inferred by a linear interpolation between neighboring bins with a measured intensity.
Binning followed by a linear interpolation to impute
values for empty elements (m/z bins) within a user-definable proximity to
non-empty elements while stetting the element's value to the
baselevel
otherwise. See impute = "linbase"
parameter of
imputeLinInterpol
for more details.
Set the elements' values to the integral of the linearly interpolated data from plus to minus half the step size.
profMat
returns the profile matrix (rows representing scans,
columns equally spaced m/z values).
From xcms
version 1.51.1 on only the profMat
method
should be used to extract the profile matrix instead of the previously
default way to access it directly via object@env$profile
.
Johannes Rainer
xcmsRaw
, binYonX
and
imputeLinInterpol
for the employed binning and
missing value imputation methods, respectively.
profMat,XCMSnExp-method
for the method on
XCMSnExp
objects.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | file <- system.file('cdf/KO/ko15.CDF', package = "faahKO")
## Load the data without generating the profile matrix (profstep = 0)
xraw <- xcmsRaw(file, profstep = 0)
## Extract the profile matrix
profmat <- profMat(xraw, step = 0.3)
dim(profmat)
## If not otherwise specified, the settings from the xraw object are used:
profinfo(xraw)
## To extract a profile matrix with linear interpolation use
profmat <- profMat(xraw, step = 0.3, method = "binlin")
## Alternatively, the profMethod of the xraw objects could be changed
profMethod(xraw) <- "binlin"
profmat_2 <- profMat(xraw, step = 0.3)
all.equal(profmat, profmat_2)
|
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