MSdata-class: Simple MS data object
In jotsetung/xcmsExtensions: Extensions to the xcms package
Description
Usage
Arguments
Value
Objects of the class
Slots
Constructors and alike
Accessing data of an MSdata object
Data visualizations
Data manipulations
Author(s)
References
See Also
Examples
Description
The MSdata is a simple object to store intensity values for m/z
- retention time tuples from a complete or only a subset of an MS run.
Usage
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## S4 method for signature 'MSdata'
as.matrix(x, ...)
## S4 method for signature 'MSdata'
binMz(object, FUN=max, bins=NULL, nbin=NULL,
binSize=NULL)
## S4 method for signature 'MSdata'
binMzRtime(object, FUN=max, mzNbin=NULL,
mzBinSize=NULL, rtNbin=NULL, rtBinSize=NULL)
## S4 method for signature 'MSdata'
binRtime(object, FUN=max, bins=NULL, nbin=NULL,
binSize=NULL)
## S4 method for signature 'MSdata'
chromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, add=FALSE,
main=paste(format(mzrange(object),
2), collapse="-"),
xlab="Retention time", ylab="Intensity", ...)
## S4 method for signature 'MSdata'
getChromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, ...)
## S4 method for signature 'MSdata'
getSpectrum(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, ...)
## S4 method for signature 'MSdata'
intensity(object)
## S4 replacement method for signature 'MSdata'
intensity(object) <- value
## S4 method for signature 'MSdata'
intrange(object)
## S4 method for signature 'MSdata'
mapMatrix(object)
MSdata(mz, rtime, intensity, mslevel=1)
## S4 method for signature 'xcmsRaw'
msData(object, mzrange=NULL, rtrange=NULL, ...)
## S4 method for signature 'MSdata'
mz(object)
## S4 replacement method for signature 'MSdata'
mz(object) <- value
## S4 method for signature 'MSdata'
mzrange(object)
## S4 method for signature 'MSdata'
plotChromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, add=FALSE,
main=paste(format(mzrange(object),
2), collapse="-"),
xlab="Retention time", ylab="Intensity", ...)
## S4 method for signature 'MSdata'
plotSpectrum(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, add=FALSE,
main=paste(format(rtrange(object),
2), collapse="-"),
xlab="M/Z", ylab="Intensity", ...)
## S4 method for signature 'MSdata'
rtime(object, return.type="numeric")
## S4 replacement method for signature 'MSdata'
rtime(object) <- value
## S4 method for signature 'MSdata'
rtrange(object)
## S4 method for signature 'MSdata'
subset(x, mzrange=NULL, rtrange=NULL)
Arguments
(in alphabetic order)
add
For plotChromatogram and plotSpectrum: if the plot should be added to an
existing plot.
bins
For getChromatogram, getSpectrum,
plotChromatogram, plotSpectrum, binMz and binRtime:
Numeric vector specifying the bins to bin the retention time. See
getChromatogram method description for details on the
binning.
binSize
For getChromatogram, getSpectrum,
plotChromatogram, plotSpectrum, binMz and binRtime:
Numeric (length 1) specifying the bin width/size. See
getChromatogram method description for details on the
binning.
FUN
For getChromatogram, getSpectrum,
plotChromatogram, plotSpectrum, binMz,
binMzRtime and binRtime: function
that should be used to aggregate intensities within a bin. By
default the largest intensity within a bin is selected. See
getChromatogram method description for details on the
binning.
intensity
A numeric vector specifying the intensity values.
main
For plotChromatogram and plotSpectrum: the title for the plot.
mslevel
For MSdata: the MS level.
mz
A numeric vector specifying the m/z values.
mzNbin
For binMzRtime: numeric (length 1) specifying the number of
bins to bin the M/Z range. See also argument bin.
mzBinSize
For binMzRtime: numeric (length 1) specifying the size of
the bins along M/Z range. See also argument binSize.
mzrange
For msData and subset: a numeric of length 2
specifying the range of m/z values to be extracted from the object.
nbin
For getChromatogram, getSpectrum,
plotChromatogram, plotSpectrum, binMz and
binRtime: numeric
(length 1) specifying the number of bins in which the retention time
range (or M/Z range) should be binned. See getChromatogram method
description for details on the binning.
object
For all methods a MSdata object.
return.type
For rtime: either "numeric" or "Rle" to return
the retention time as a numeric vector, or as a
Rle object.
rtime
A numeric vector specifying the retention time values.
rtNbin
For binMzRtime: numeric (length 1) specifying the number of
bins to bin the retention time range. See also argument bin.
rtBinSize
For binMzRtime: numeric (length 1) specifying the size of
the bins along retention time range. See also argument binSize.
rtrange
For msData and subset: a numeric of length 2
specifying the retention time range to be extracted from the object.
value
For intensity<-, mz<- and rtime<-, a numeric
vector with the intensity, mz or retention time values,
respectively.
x
For as.matrix and subset: a MSdata object.
xlab
For plotChromatogram and plotSpectrum: the label for the x-axis.
ylab
For plotChromatogram and plotSpectrum: the label for the y-axis.
...
For plotChromatogram and plotSpectrum: additional graphical properties to be
passed to the plot function.
For all other methods: not used.
Value
Refer to the method and function description above for detailed
information on the returned result object.
Objects of the class
MSdata objects are created by the constructor function
MSdata, or the msData method e.g. to extract data from
an xcmsRaw object.
Slots
- intensity
-
An integer vector with the intensities for each m/z - retention
time tuple.
- intrange
-
A numeric vector of length 2 representing the range of intensity
values.
- mslevel
-
The MS level.
- mz
-
A numeric vector with the m/z values.
- mzrange
-
A numeric vector of length 2 specifying the range of m/z
values.
- rtime
-
An Rle object with the retention time values.
- rtrange
-
A numeric vector of length 2 specifying the retention time range.
Constructors and alike
- MSdata
-
Constructor method to create a new MSdata instance.
- msData
-
Extract MS data from an xcmsRaw object and
return the values as a MSdata object. Arguments
mzrange and rtrange allow to define the data sub-set
to be extracted. If not specified, the method will extract the
full data.
Accessing data of an MSdata object
- as.matrix
-
Extracts a matrix with column names "rtime", "mz" and
"intensity" with all data values of the MSdata
object.
- getChromatogram
-
Extracts the chromatogram from the MSdata (i.e. intensities
along the retention time dimension). The method returns a numeric
matrix with two columns, "rtime" and
"intensity", the rows being ordered increasingly by
retention time.
Since the MSdata is in principle
3-dimensional (intensities in the m/z - rt space), values have to
be aggregated in the m/z dimension. By default the method only
aggregates intensities along the m/z dimension with the same
retention time value. Specifying either one of bins,
nbin and binSize it is in addition possible to
bin the retention times into discrete, equal spaced, bins. Thus,
all intensities falling into one bin (i.e. retention time within
the bin and all intensities along the m/z dimension present in the
MSdata) are aggregated using the function FUN, which
by default just selects the maximal signal in each bin.
The binning in rt-dimension is performed as follows: if
nbins is specified, the range of retention times
(rtrange) is split into nbins equal sized bins and
all intensities with an retention time within a certain bin are
aggregated (including all in m/z dimension; within
mzrange). For binSize, the range is split into bins
with the width/size binSize. Argument bins allows to
define the bins externally and thus ensure an identical binning
e.g. across MSdata objects from different samples.
How the aggregation of intensity values along the m/z range (and
eventually also for retention times within the same retention time
bin) is performed can be specified with the FUN
argument. By default, the maximal signal is selected
(i.e. FUN=max). For a MSdata object representing a full MS
run, this would correspond to a base peak chromatogram
(BPC), while using FUN=sum would result in an total
ion chromatogram (TIC) [Smith 2014].
getSpectrum
Extracts the spectrum from the MSdata (i.e. intensities
along the M/Z dimension, usually for a single retention time or a
small retention time range). The method returns a numeric matrix
with two columns, "mz" and "intensity" with the rows
being increasingly ordered by the mz value.
By default, the method aggregates all intensity values along the
retention time dimension (available in the MSdata object)
for a single M/Zvalue. The argument FUN allows to specify
the function that should be used to aggregate intensities.
In addition, the arguments bins, nbin and
binSize allow to bin M/Z values and thus to aggregate also
intensity values of M/Z values falling within a certain bin. See
the documentation of the getChromatogram method above for
more details.
- intensity, intensity<-
-
Get or set the intensity values of the MSdata
object. intensity returns the intensity values.
- intrange
-
Get the intensity value range. Returns a numeric vector of length
2. For an empty MSdata object without data points it
returns c(NA, NA).
- mapMatrix
-
Extract the MS data as a two-dimensional matrix, columns being the
(discrete) retention time of each measurement, rows its M/Z
value. The method returns a sparse matrix from the
Matrix package with not-present intentensity values encoded
by a 0 (i.e. if for a specific retention time - M/Z tuple
no intensity is available/was measured). The sparseness of
the data matrix might be reduced by performing first a binning in
M/Z, retention time or both dimensions.
The rownames of the matrix represent the M/Z intensities, the
column names the retention time values.
- mz, mz<-
-
Get or set the mz values of the MSdata object. mz
returns a numeric vector with the mz values.
- mzrange
-
Get the m/z value range of the MSdata object. Returns a
numeric vector of 2 or c(NA, NA) if the object is empty.
- rtime, rtime<-
-
Get or set the retention times of the MSdata
object. Depending on the return.type argument, the
retention time is returned as a numeric vector or as an
Rle object.
- rtrange
-
Get the retention time range of the MSdata object. Returns a
numeric vector of 2 or c(NA, NA) if the object is empty.
- subset
-
Subset the MSdata object based on the probided ranges in
M/Z and/or retention time dimension. The method returns a
MSdata object.
Data visualizations
- chromatogram
-
See plotChromatogram below.
- plotChromatogram
-
The method plots the chromatogram of an MSdata
object which is internally extracted by the getChromatogram
method (refer to the description of that function for the data
binning etc.).
- plotSpectrum
-
The method plots the spectrum of an MSdata
object which is internally extracted by the getSpectrum
method (refer to the description of that function for the data
binning etc.).
Data manipulations
- binMz
-
This method cuts the M/Z range of an MSdata object in equal
spaced bins and aggregates all intensity values with an M/Z value
falling within the bin and the same retention time.
For details on the method arguments and the binning see the help
for the getChromatogram method.
The method returns an MSdata object.
- binMzRtime
-
This method performs a binning first in M/Z dimension followed by
a retention time binning.
For details on binning see the getChromatogram method.
The method returns a MSdata object with the data binned
both on M/Z and retention time dimension.
- binRtime
-
Same as the binMz method, but for binning along the
retention time dimension.
The method returns an MSdata object.
Author(s)
Johannes Rainer.
References
Smith R, Mathis AD, Ventura D and Prince JT. (2014) Proteomics,
lipidomics, metabolomics: a mess spectrometry tutorial from a computer
scientists's point of view. BMC Bioinformatics, 15(Suppl 7):59.
See Also
Examples
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## Load the faahKO package with the test data for the xcms package.
library(faahKO)
xset <- faahko
## Get the raw data for the first sample.
xraw <- getXcmsRaw(xset, 1)
## Define a data sub-set and extract the corresponding values.
rtr <- c(2600, 2670)
mzr <- c(300, 400)
mssub <- msData(xraw, rtrange=rtr, mzrange=mzr)
## Get the mz value and retention time range
mzrange(mssub)
rtrange(mssub)
## The actual retention time range is different from the specifyed
## range as it depends on the acutally measured scan times.
## Get the intensity range
intrange(mssub)
## Get mz values, retention times and intensities.
head(mz(mssub))
head(rtime(mssub))
head(intensity(mssub))
## Extract a matrix with the full data.
head(as.matrix(mssub))
## Extracting the chromatogram from an MSdata.
## Defining the mz and rt ranges. These correspond approx. to the
## peak in the xcms vignette (Figure 4).
mzr <- c(302, 302.5)
rtr <- c(2500, 2700)
msd <- msData(xraw, rtrange=rtr, mzrange=mzr)
## How many data points do we have?
length(rtime(msd))
## Hom many unique retention times?
length(unique(rtime(msd)))
## Thus, we have some intensities with the same retention time (but different
## m/z).
####-------------
## Extracting the chromatogram.
chr <- getChromatogram(msd)
nrow(chr)
## By default, the method aggregates intensities with identical retention time.
## Plotting the chromatogram
plotChromatogram(msd, type="l")
## Next we extract a chromatogram with binning on the retention time. Thus we
## set to split the retention time range into 50 equal spaced bins and to aggregate
## the intensities within each of the bins. As aggregation function we use "max", i.e.
## we select the maximal intensity for each bin.
chr2 <- getChromatogram(msd, FUN=max, nbin=50)
nrow(chr2)
## Adding that chromatogram to the existing plot.
plotChromatogram(msd, FUN=max, nbin=50, add=TRUE, col="blue", type="b")
## Generating the base peak chromatogram (BPC) and the total ion chromatogram (TIC)
fulld <- msData(xraw)
par(mfrow=c(1, 2))
plotChromatogram(fulld, FUN=max, type="l", main="BPC")
plotChromatogram(fulld, FUN=sum, type="l", main="TIC")
####-------------
## Extract a spectrum.
## Similar to the getChromatogram example above we can simply extract a
## spectrum using the getSpectrum method.
spc <- getSpectrum(msd)
nrow(spc)
## The spectrum for this peak is rather small, which is not surprising, since
## we restricted the m/z range. To get the spectrum for the compound corresponding
## to the peak, we restrict a narrow retention time range around the peak, and a
## larget mz range.
rtr <- c(2560, 2640)
mzr <- c(300, 330)
## Get the "slice" of MS data defined by this ranges
msd <- msData(xraw, mzrange=mzr, rtrange=rtr)
## Get the (unbinned) spectrum; intensities with the same m/z but different
## retention times are aggregated (i.e. the maximal signal is taken).
spc <- getSpectrum(msd)
nrow(spc)
## Next we plot the chromatogram and the spectrum for the MS data slice.
par(mfrow=c(1, 2))
plotChromatogram(msd, type="l")
plotSpectrum(msd, type="l")
## Extract the data as a two-dimensional matrix.
mapM <- mapMatrix(msd)
dim(mapM)
head(mapM)
####-------------
## Data manipulations
## We process the MSdata object from above and aggregate values falling into
## the same bin on M/Z dimension. We define a binSize of 1, thus, the maximum
## of all signal values with the same retention time falling into the same bin
## will be returned in the resulting MSdata object. Note that this binning is
## rather crude and we should use this only e.g. for plotting purposes, i.e. to
## reduce the data points to plot.
msd
msdBinned <- binMz(msd, binSize=1)
msdBinned
length(unique(mz(msd)))
length(unique(mz(msdBinned)))
## Plot the spectrum and the chromatogram of both.
par(mfrow=c(1, 2))
plotSpectrum(msd, type="l")
plotSpectrum(msdBinned, type="l", add=TRUE, col="blue")
plotChromatogram(msd, type="l")
plotChromatogram(msdBinned, type="l", add=TRUE, col="blue", lty=2)
## The same way we perform the binning in retention time axis.
msdBinned <- binRtime(msd, binSize=5)
length(unique(rtime(msd)))
length(unique(rtime(msdBinned)))
## Plot the spectrum and the chromatogram of both.
par(mfrow=c(1, 2))
plotSpectrum(msd, type="l")
plotSpectrum(msdBinned, type="l", add=TRUE, col="blue", lty=2)
plotChromatogram(msd, type="l")
plotChromatogram(msdBinned, type="l", add=TRUE, col="blue", lty=2)
## Next we bin the data in both dimensions.
binBoth <- binMzRtime(msd, mzNbin=20, rtBinSize=5)
binBoth
jotsetung/xcmsExtensions documentation built on May 19, 2019, 9:42 p.m.
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Description Usage Arguments Value Objects of the class Slots Constructors and alike Accessing data of an MSdata object Data visualizations Data manipulations Author(s) References See Also Examples
Description
The MSdata is a simple object to store intensity values for m/z
- retention time tuples from a complete or only a subset of an MS run.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 | ## S4 method for signature 'MSdata'
as.matrix(x, ...)
## S4 method for signature 'MSdata'
binMz(object, FUN=max, bins=NULL, nbin=NULL,
binSize=NULL)
## S4 method for signature 'MSdata'
binMzRtime(object, FUN=max, mzNbin=NULL,
mzBinSize=NULL, rtNbin=NULL, rtBinSize=NULL)
## S4 method for signature 'MSdata'
binRtime(object, FUN=max, bins=NULL, nbin=NULL,
binSize=NULL)
## S4 method for signature 'MSdata'
chromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, add=FALSE,
main=paste(format(mzrange(object),
2), collapse="-"),
xlab="Retention time", ylab="Intensity", ...)
## S4 method for signature 'MSdata'
getChromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, ...)
## S4 method for signature 'MSdata'
getSpectrum(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, ...)
## S4 method for signature 'MSdata'
intensity(object)
## S4 replacement method for signature 'MSdata'
intensity(object) <- value
## S4 method for signature 'MSdata'
intrange(object)
## S4 method for signature 'MSdata'
mapMatrix(object)
MSdata(mz, rtime, intensity, mslevel=1)
## S4 method for signature 'xcmsRaw'
msData(object, mzrange=NULL, rtrange=NULL, ...)
## S4 method for signature 'MSdata'
mz(object)
## S4 replacement method for signature 'MSdata'
mz(object) <- value
## S4 method for signature 'MSdata'
mzrange(object)
## S4 method for signature 'MSdata'
plotChromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, add=FALSE,
main=paste(format(mzrange(object),
2), collapse="-"),
xlab="Retention time", ylab="Intensity", ...)
## S4 method for signature 'MSdata'
plotSpectrum(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, add=FALSE,
main=paste(format(rtrange(object),
2), collapse="-"),
xlab="M/Z", ylab="Intensity", ...)
## S4 method for signature 'MSdata'
rtime(object, return.type="numeric")
## S4 replacement method for signature 'MSdata'
rtime(object) <- value
## S4 method for signature 'MSdata'
rtrange(object)
## S4 method for signature 'MSdata'
subset(x, mzrange=NULL, rtrange=NULL)
|
Arguments
(in alphabetic order)
add |
For |
bins |
For |
binSize |
For |
FUN |
For |
intensity |
A numeric vector specifying the intensity values. |
main |
For |
mslevel |
For |
mz |
A numeric vector specifying the m/z values. |
mzNbin |
For |
mzBinSize |
For |
mzrange |
For |
nbin |
For |
object |
For all methods a |
return.type |
For |
rtime |
A numeric vector specifying the retention time values. |
rtNbin |
For |
rtBinSize |
For |
rtrange |
For |
value |
For |
x |
For |
xlab |
For |
ylab |
For |
... |
For For all other methods: not used. |
Value
Refer to the method and function description above for detailed information on the returned result object.
Objects of the class
MSdata objects are created by the constructor function
MSdata, or the msData method e.g. to extract data from
an xcmsRaw object.
Slots
- intensity
-
An integer vector with the intensities for each m/z - retention time tuple.
- intrange
-
A numeric vector of length 2 representing the range of intensity values.
- mslevel
-
The MS level.
- mz
-
A numeric vector with the m/z values.
- mzrange
-
A numeric vector of length 2 specifying the range of m/z values.
- rtime
-
An
Rleobject with the retention time values. - rtrange
-
A numeric vector of length 2 specifying the retention time range.
Constructors and alike
- MSdata
-
Constructor method to create a new
MSdatainstance. - msData
-
Extract MS data from an
xcmsRawobject and return the values as aMSdataobject. Argumentsmzrangeandrtrangeallow to define the data sub-set to be extracted. If not specified, the method will extract the full data.
Accessing data of an MSdata object
- as.matrix
-
Extracts a matrix with column names
"rtime","mz"and"intensity"with all data values of theMSdataobject. - getChromatogram
-
Extracts the chromatogram from the
MSdata(i.e. intensities along the retention time dimension). The method returns a numeric matrix with two columns,"rtime"and"intensity", the rows being ordered increasingly by retention time.Since the
MSdatais in principle 3-dimensional (intensities in the m/z - rt space), values have to be aggregated in the m/z dimension. By default the method only aggregates intensities along the m/z dimension with the same retention time value. Specifying either one ofbins,nbinandbinSizeit is in addition possible to bin the retention times into discrete, equal spaced, bins. Thus, all intensities falling into one bin (i.e. retention time within the bin and all intensities along the m/z dimension present in theMSdata) are aggregated using the functionFUN, which by default just selects the maximal signal in each bin.The binning in rt-dimension is performed as follows: if
nbinsis specified, the range of retention times (rtrange) is split intonbinsequal sized bins and all intensities with an retention time within a certain bin are aggregated (including all in m/z dimension; withinmzrange). ForbinSize, the range is split into bins with the width/sizebinSize. Argumentbinsallows to define the bins externally and thus ensure an identical binning e.g. acrossMSdataobjects from different samples.How the aggregation of intensity values along the m/z range (and eventually also for retention times within the same retention time bin) is performed can be specified with the
FUNargument. By default, the maximal signal is selected (i.e.FUN=max). For aMSdataobject representing a full MS run, this would correspond to a base peak chromatogram (BPC), while usingFUN=sumwould result in an total ion chromatogram (TIC) [Smith 2014].
getSpectrum
Extracts the spectrum from the MSdata (i.e. intensities
along the M/Z dimension, usually for a single retention time or a
small retention time range). The method returns a numeric matrix
with two columns, "mz" and "intensity" with the rows
being increasingly ordered by the mz value.
By default, the method aggregates all intensity values along the
retention time dimension (available in the MSdata object)
for a single M/Zvalue. The argument FUN allows to specify
the function that should be used to aggregate intensities.
In addition, the arguments bins, nbin and
binSize allow to bin M/Z values and thus to aggregate also
intensity values of M/Z values falling within a certain bin. See
the documentation of the getChromatogram method above for
more details.
- intensity, intensity<-
-
Get or set the intensity values of the
MSdataobject.intensityreturns the intensity values. - intrange
-
Get the intensity value range. Returns a numeric vector of length 2. For an empty
MSdataobject without data points it returnsc(NA, NA). - mapMatrix
-
Extract the MS data as a two-dimensional matrix, columns being the (discrete) retention time of each measurement, rows its M/Z value. The method returns a sparse matrix from the
Matrixpackage with not-present intentensity values encoded by a0(i.e. if for a specific retention time - M/Z tuple no intensity is available/was measured). The sparseness of the data matrix might be reduced by performing first a binning in M/Z, retention time or both dimensions.The rownames of the matrix represent the M/Z intensities, the column names the retention time values.
- mz, mz<-
-
Get or set the mz values of the
MSdataobject.mzreturns a numeric vector with the mz values. - mzrange
-
Get the m/z value range of the
MSdataobject. Returns a numeric vector of 2 orc(NA, NA)if the object is empty. - rtime, rtime<-
-
Get or set the retention times of the
MSdataobject. Depending on thereturn.typeargument, the retention time is returned as a numeric vector or as anRleobject. - rtrange
-
Get the retention time range of the
MSdataobject. Returns a numeric vector of 2 orc(NA, NA)if the object is empty. - subset
-
Subset the
MSdataobject based on the probided ranges in M/Z and/or retention time dimension. The method returns aMSdataobject.
Data visualizations
- chromatogram
-
See
plotChromatogrambelow. - plotChromatogram
-
The method plots the chromatogram of an
MSdataobject which is internally extracted by thegetChromatogrammethod (refer to the description of that function for the data binning etc.). - plotSpectrum
-
The method plots the spectrum of an
MSdataobject which is internally extracted by thegetSpectrummethod (refer to the description of that function for the data binning etc.).
Data manipulations
- binMz
-
This method cuts the M/Z range of an
MSdataobject in equal spaced bins and aggregates all intensity values with an M/Z value falling within the bin and the same retention time.For details on the method arguments and the binning see the help for the
getChromatogrammethod.The method returns an
MSdataobject. - binMzRtime
-
This method performs a binning first in M/Z dimension followed by a retention time binning.
For details on binning see the
getChromatogrammethod.The method returns a
MSdataobject with the data binned both on M/Z and retention time dimension. - binRtime
-
Same as the
binMzmethod, but for binning along the retention time dimension.The method returns an
MSdataobject.
Author(s)
Johannes Rainer.
References
Smith R, Mathis AD, Ventura D and Prince JT. (2014) Proteomics, lipidomics, metabolomics: a mess spectrometry tutorial from a computer scientists's point of view. BMC Bioinformatics, 15(Suppl 7):59.
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 | ## Load the faahKO package with the test data for the xcms package.
library(faahKO)
xset <- faahko
## Get the raw data for the first sample.
xraw <- getXcmsRaw(xset, 1)
## Define a data sub-set and extract the corresponding values.
rtr <- c(2600, 2670)
mzr <- c(300, 400)
mssub <- msData(xraw, rtrange=rtr, mzrange=mzr)
## Get the mz value and retention time range
mzrange(mssub)
rtrange(mssub)
## The actual retention time range is different from the specifyed
## range as it depends on the acutally measured scan times.
## Get the intensity range
intrange(mssub)
## Get mz values, retention times and intensities.
head(mz(mssub))
head(rtime(mssub))
head(intensity(mssub))
## Extract a matrix with the full data.
head(as.matrix(mssub))
## Extracting the chromatogram from an MSdata.
## Defining the mz and rt ranges. These correspond approx. to the
## peak in the xcms vignette (Figure 4).
mzr <- c(302, 302.5)
rtr <- c(2500, 2700)
msd <- msData(xraw, rtrange=rtr, mzrange=mzr)
## How many data points do we have?
length(rtime(msd))
## Hom many unique retention times?
length(unique(rtime(msd)))
## Thus, we have some intensities with the same retention time (but different
## m/z).
####-------------
## Extracting the chromatogram.
chr <- getChromatogram(msd)
nrow(chr)
## By default, the method aggregates intensities with identical retention time.
## Plotting the chromatogram
plotChromatogram(msd, type="l")
## Next we extract a chromatogram with binning on the retention time. Thus we
## set to split the retention time range into 50 equal spaced bins and to aggregate
## the intensities within each of the bins. As aggregation function we use "max", i.e.
## we select the maximal intensity for each bin.
chr2 <- getChromatogram(msd, FUN=max, nbin=50)
nrow(chr2)
## Adding that chromatogram to the existing plot.
plotChromatogram(msd, FUN=max, nbin=50, add=TRUE, col="blue", type="b")
## Generating the base peak chromatogram (BPC) and the total ion chromatogram (TIC)
fulld <- msData(xraw)
par(mfrow=c(1, 2))
plotChromatogram(fulld, FUN=max, type="l", main="BPC")
plotChromatogram(fulld, FUN=sum, type="l", main="TIC")
####-------------
## Extract a spectrum.
## Similar to the getChromatogram example above we can simply extract a
## spectrum using the getSpectrum method.
spc <- getSpectrum(msd)
nrow(spc)
## The spectrum for this peak is rather small, which is not surprising, since
## we restricted the m/z range. To get the spectrum for the compound corresponding
## to the peak, we restrict a narrow retention time range around the peak, and a
## larget mz range.
rtr <- c(2560, 2640)
mzr <- c(300, 330)
## Get the "slice" of MS data defined by this ranges
msd <- msData(xraw, mzrange=mzr, rtrange=rtr)
## Get the (unbinned) spectrum; intensities with the same m/z but different
## retention times are aggregated (i.e. the maximal signal is taken).
spc <- getSpectrum(msd)
nrow(spc)
## Next we plot the chromatogram and the spectrum for the MS data slice.
par(mfrow=c(1, 2))
plotChromatogram(msd, type="l")
plotSpectrum(msd, type="l")
## Extract the data as a two-dimensional matrix.
mapM <- mapMatrix(msd)
dim(mapM)
head(mapM)
####-------------
## Data manipulations
## We process the MSdata object from above and aggregate values falling into
## the same bin on M/Z dimension. We define a binSize of 1, thus, the maximum
## of all signal values with the same retention time falling into the same bin
## will be returned in the resulting MSdata object. Note that this binning is
## rather crude and we should use this only e.g. for plotting purposes, i.e. to
## reduce the data points to plot.
msd
msdBinned <- binMz(msd, binSize=1)
msdBinned
length(unique(mz(msd)))
length(unique(mz(msdBinned)))
## Plot the spectrum and the chromatogram of both.
par(mfrow=c(1, 2))
plotSpectrum(msd, type="l")
plotSpectrum(msdBinned, type="l", add=TRUE, col="blue")
plotChromatogram(msd, type="l")
plotChromatogram(msdBinned, type="l", add=TRUE, col="blue", lty=2)
## The same way we perform the binning in retention time axis.
msdBinned <- binRtime(msd, binSize=5)
length(unique(rtime(msd)))
length(unique(rtime(msdBinned)))
## Plot the spectrum and the chromatogram of both.
par(mfrow=c(1, 2))
plotSpectrum(msd, type="l")
plotSpectrum(msdBinned, type="l", add=TRUE, col="blue", lty=2)
plotChromatogram(msd, type="l")
plotChromatogram(msdBinned, type="l", add=TRUE, col="blue", lty=2)
## Next we bin the data in both dimensions.
binBoth <- binMzRtime(msd, mzNbin=20, rtBinSize=5)
binBoth
|
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