MSslice-class: MS data subsets of several samples
In jotsetung/xcmsExtensions: Extensions to the xcms package
Description
Usage
Arguments
Value
Objects of the class
Slots
Extends
Constructors and alike
Accessing and subsetting
Data visualizations
Data manipulations
Author(s)
See Also
Examples
Description
Sub-sets of an MS run across several samples can be stored in a
MSslice object. Such a slice of the MS data is defined by an
m/z and a retention time range in each sample. The actual data of the
slice in each sample is stored as MSdata object, i.e. as
intensities for each mz/rt tuple measured in a sample.
Depending on the measurements, the actual mz/rt ranges in each
individual MSdata can be slightly different, but all are
within the mz and rt range of the MSslice object (that can be
returned by the mzrange and rtrange method).
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
82
83
84
85
86
## S4 method for signature 'MSslice'
assayData(object)
## S4 replacement method for signature 'MSslice'
assayData(object) <- value
## S4 method for signature 'MSslice'
binMzRtime(object, FUN=max, mzNbin=NULL,
mzBinSize=NULL, rtNbin=NULL, rtBinSize=NULL)
## S4 method for signature 'MSslice'
binRtime(object, FUN=max, bins=NULL, nbin=NULL,
binSize=NULL)
## S4 method for signature 'MSslice'
getChromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, ...)
## S4 method for signature 'MSslice'
getSpectrum(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, ...)
## S4 method for signature 'MSslice'
intrange(object)
## S4 method for signature 'MSslice'
length(x)
MSslice(x, ...)
## S4 method for signature 'MSslice'
msData(object, ...)
## S4 method for signature 'list'
msSlice(object, ...)
## S4 method for signature 'MSdata'
msSlice(object, ...)
## S4 method for signature 'xcmsSet'
msSlice(object, mzrange=NULL, rtrange=NULL,
rt="corrected", BPPARAM=MulticoreParam())
## S4 method for signature 'xcmsRaw'
msSlice(object, mzrange=NULL, rtrange=NULL, ...)
## S4 method for signature 'MSslice'
mzrange(object)
## S4 method for signature 'MSslice'
names(x)
## S4 replacement method for signature 'MSslice'
names(x) <- value
## S4 method for signature 'MSslice'
phenoData(object)
## S4 replacement method for signature 'MSslice'
phenoData(object) <- value
## S4 method for signature 'MSslice'
pData(object)
## S4 replacement method for signature 'MSslice'
pData(object) <- value
## S4 method for signature 'MSslice'
plotChromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL,
main=paste(format(mzrange(object), 2),
collapse="-"), xlab="Retention time",
ylab="Intensity", col=1, lty=1, ...)
## S4 method for signature 'MSslice'
plotSpectrum(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL,
main=paste(format(rtrange(object), 2),
collapse="-"), xlab="M/Z",
ylab="Intensity", col=1, lty=1, ...)
## S4 method for signature 'MSslice'
rtrange(object)
## S4 method for signature 'MSslice'
subset(x, mzrange=NULL, rtrange=NULL)
Arguments
(in alphabetic order)
bins
For getChromatogram, getSpectrum,
plotChromatogram, plotSpectrum, binMz and binRtime: numeric
vector specifying the bins to bin the retention time. See
getChromatogram method description for MSdata
objects for more 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 MSdata
objects for more 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 MSdata
objects for more details on the binning.
BPPARAM
Parallel processing parameters; see
bpparam for more information. Note that
parallel processing will most likely not work with the snow,
thus, on Windows machines there will no parallel processing be
available.
col
For plotChromatogram and plotSpectrum: a single color or vector specifying
colors for each sample/MSdata object in the MSslice.
lty
For plotChromatogram and plotSpectrum: a numeric specifying the line type for
each sample/MSdata object in the MSslice; if
lty has length of 1, this line type will be used for all
lines.
main
For plotChromatogram and plotSpectrum: the title of the plot.
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
A numeric vector defining the m/z-value range of the slice.
nbin
For getChromatogram, getSpectrum,
plotChromatogram, plotSpectrum, binMz and binRtime: numeric
(length 1) specifying the number of bins in which the retention time
range should be binned. See getChromatogram method
description for MSdata objects for more details on the
binning.
object
For msSlice: either a list of MSdata
objects, an xcmsSet or
xcmsRaw object.
For all other methods a MSslice object.
rt
For msSlice: either "raw" or "corrected" to
specify whether the raw or retention-time corrected scan times
should be used.
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
A numeric vector defining the retention time range of the slice.
value
For names: a character vector (length matching the number of
MSdata objects in the @assayData slot) specifying
names of the individual objects.
For assayData: a MSdata object or a list
of such objects.
For phenoData: a data.frame or
AnnotatedDataFrame providing the phenotypic annotation of the
samples (covariates etc).
For pData: a data.frame providing the phenotypic
annotation of the samples.
x
For length, names and subset: an MSslice
object.
For MSslice: a MSdata or a list of MSdata objects.
xlab
For plotChromatogram and plotSpectrum: the label for the x-axis.
ylab
For plotChromatogram and plotSpectrum: the label for the y-axis.
...
For MSslice: additional arguments passed to the constructor
(i.e. experimentData or phenoData).
For plotChromatogram: additional graphical parameters to be
passed down to the base plot function.
Ignored for all other methods.
Value
Refer to the method and function description above for detailed
information on the returned result object.
Objects of the class
While MSslice objects can be created by the constructor
function MSslice the default way to create such an object is by
using the msSlice method on an xcmsSet (or
xcmsRaw) object.
Slots
- assayData
-
A list of MSdata objects.
- experimentData
-
Object of class MIAPE containing details of
experimental methods.
- mzrange
-
A numeric vector of length 2 specifying the range of m/z
values of the slice.
- phenoData
-
An AnnoatedDataFrame providing the sample description.
- rtrange
-
A numeric vector of length 2 specifying the retention time range
of the slice.
Extends
Class "Versioned" defined in the Biobase package, directly.
Constructors and alike
- MSslice
-
Constructor method to create a new MSslice instance
accepting either a list of MSdata objects or
a single MSdata object. All additional arguments
(e.g. phenoData, experimentData)
are directly passed to the "new" call.
- msSlice
-
Extract an msSlice object from an
xcmsRaw or xcmsSet
object. The latter (i.e. extraction from an xcmsSet object)
is the default constructor that will be mostly used. It
allows to extract intensity values for the m/z and rt range that
defines the slice of MS data from each individual sample. The
result is returned as an MSslice object. If multiple mz and
rt ranges are specified (i.e. arguments mzrange and
rtrange are 2-column matrices, each row specifying a
different range) the result will be returned as an
MSsliceList object.
Note that the mzrange and rtrange of each of the
extracted MSdata for each sample will be slightly
different, but all are within the mzrange and
rtrange of the MSslice object.
If object is an MSdata object it wraps that into an
MSslice object.
Accessing and subsetting
- assayData,assayData<-
-
Get and set the assay data (i.e. the list of internal
MSdata objects). This method is the same than the
msData method.
- getChromatogram
-
Extracts a numeric matrix with the chromatogram (i.e. intensities
along the retention time dimension) for each of the MSdata
object and hence samples of the MSslice object. The
rownames of the matrix represent the (unique) retention times and
each column contains the spectrum of one sample/MSdata
object (i.e. the intensities aggregated in m/z direction for the
respective retention time using the aggregation function specified
with argument FUN).
In the default settings, without specifying any of the arguments
bins, nbin or binSize, the method returns a
matrix with one row for each unique retention time across all of
the samples. Each row will only contain a numeric value for a
sample in which a signal was measured for that specific retention
time. In most instances it will be better to specify nbin
or binSize, to bin values also along the retention time
dimension. Ideally, the binning should not be too coarse, but also
not too detailed (in which case the matrix will again be
relatively sparse); a binning with a binSize=1 (i.e. one
second), or slightly smaller, might be OK in most instances.
For more details on the binning see the help for the
getChromatogram method of MSdata objects.
- getSpectrum
-
Extracts a numeric matrix with the spectrum (i.e. intensities
along the M/Z dimension) for each of the MSdata objects and
hence samples of the MSslice object. The rownames of the
matrix represent the distinct M/Z values and columns the
individual samples. For more details (e.g. also on binning etc)
see the help of the getChromatogram method above.
- intrange
-
Get the range of intensity values of the slice. This represents the range of
values across all samples (i.e. all MSdata objects within
the MSslice). Returns a numeric of length
2, or c(NA, NA) if the object is empty (or the internal
MSdata object(s) don't contain any data).
- length
-
Get the length of the object, i.e. the number of MSdata
object stored within the object.
- msData
-
Get the list of MSdata objects.
- mzrange
-
Get the m/z value range of the slice. This represents the range of
values across all samples (i.e. all MSdata objects within
the MSslice). Returns a numeric of length
2, or c(NA, NA) if the object is empty (or the internal
MSdata object(s) don't contain any data).
- names,names<-
-
Get and set the names of the MSdata objects.
- object[i]
-
Subsets the MSslice object object and returns an
MSslice object with only the elements selected by
i. i can be an integer vector or a character vector,
if names are available in object.
- object[[i]]
-
Extract e single MSdata object from the
MSslice object.
- phenoData,phenoData<-,pData,pData<-
-
Get and set the pheno data, i.e. the AnnotatedDataFrame
providing the sample annotation (phenotypic information and
covariates). Each row describing one sample each column
representing one covariate. The ordering is assumed to be
identical to the ordering of the MSdata objects in the
assayData slot.
The pData method accesses the same slot, but returns (and
accepts) a data.frame.
- rtrange
-
Get the retention time range of the slice. This represents the range of
values across all samples (i.e. all MSdata objects within
the MSslice). Returns a numeric of length
2, or c(NA, NA) if the object is empty (or the internal
MSdata object(s) don't contain any data).
- subset
-
Subset the MSslice based on the specified M/Z and retention
time ranges. The method returns a MSslice object.
Data visualizations
- plotChromatogram
-
Plots the chromatogram of the rt-m/z slice across all of the
MSdata objects (i.e. samples). The arguments col and
lty can be used to use a different color for each line
(i.e. sample) or a different line type. See description of the
getChromatogram for details on the other parameters.
- plotSpectrum
-
Plots the spectrum; see help of plotChromatogram above.
Data manipulations
- binMz
-
This method cuts the M/Z range of an MSslice 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 MSslice 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 MSslice 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 MSslice object.
Author(s)
Johannes Rainer.
See Also
xcmsSet, xcmsRaw,
MSdata, MSsliceList
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
## Load the faahKO package with the test data for the xcms package.
library(faahKO)
xset <- faahko
## Define a data sub-set and extract the corresponding values from
## the xcmsSet object. This will extract the intensity values of the
## defined slice from each individual sample.
rtr <- c(2600, 2670)
mzr <- c(300, 400)
mss <- msSlice(xset, rtrange=rtr, mzrange=mzr)
## Access the phenoData
phenoData(mss)
## Access individual columns using the $ method
mss$class
## Get the number of samples
length(mss)
## We don't have any names yet
names(mss)
## Setting the names using the ones provided by the sampnames method of the
## xcmsSet object.
names(mss) <- sampnames(xset)
names(mss)
## Subset to samples with name starting with wt
mssSub <- mss[grep(names(mss), pattern="^wt")]
names(mssSub)
## Extract a single MSdata object
mssSub[["wt18"]]
## Get the mz, rt and intensity range. This corresponds to the range of
## values of the slice across all samples.
mzrange(mss)
rtrange(mss)
intrange(mss)
## Extract the list of MSdata objects
msData(mss)
## Extract the chromatogram of a m/z-rt slice across all samples.
## Defining the mz and rt ranges for the peak in the xcms
## vignette (Figure 4).
mzr <- c(302, 302.5)
rtr <- c(2500, 2700)
mss <- msSlice(xset, rtrange=rtr, mzrange=mzr)
## We're getting a sparse matrix if we're not binning along the rt-dimension,
## since the retention times of the individual data points are slightly different
## between the samples:
head(getChromatogram(mss))
## We're next binning the values in retention time-bins of size 1 (1 second). By default
## (with FUN=max), the maximal signal is used for each bin.
chrM <- getChromatogram(mss, binSize=1)
dim(chrM)
head(chrM)
## We can also create an image from this matrix. Each column represents the chromatogram
## from one sample, each row one retention time bin with the intensity being color coded.
image(t(chrM))
## Next we plot the chromatogram of the slice across all samples.
## Without any binning:
plotChromatogram(mss, col="#00000080", type="l")
## And with binning.
plotChromatogram(mss, binSize=1, col="#00000080", type="l")
## Extracting the full MS data from the xcmsSet to create base peak chromatogram (BPC)
## and total ion chromatogram (TIC) plot of all samples.
msFull <- msSlice(xset)
## Base peak chromatogram with 1 second binning
plotChromatogram(msFull, binSize=1, col="#00000080", type="l")
## Total ion chromatogram with 1 second binning
plotChromatogram(msFull, FUN=sum, binSize=1, col="#00000080", type="l")
## Extending the M/Z range of the slice and extracting and plotting also the spectrum.
mzr <- c(300, 303)
mss <- msSlice(xset, rtrange=rtr, mzrange=mzr)
## Get the spectrum without binning:
head(getSpectrum(mss))
## We can also extract a slice from an xcmsRaw object, which will then
## contain the data only of that individual sample. Without specifying an
## mzrange and rtrange we extract the full data.
msSlice(getXcmsRaw(xset, 1))
par(mfrow=c(1, 2))
plotChromatogram(mss, binSize=1, col="#00000080", type="l")
plotSpectrum(mss, col="#00000040", type="h")
## Or from an MSdata object; extracting first a MSdata object containing
## the *full* MS data from a single file and creating then an MSslice object
## from that.
msd <- msData(getXcmsRaw(xset, 1))
msSlice(msd)
## Extracting the MSdata from the second sample and passing both to the
## MSslice constructor to generate a two-sample MSslice object.
msd2 <- msData(getXcmsRaw(xset, 2))
MSslice(list(msd, msd2))
####-------------
## Data manipulations
## We bin the MSslice object in 5 second retention time bins along the
## retention time dimension. Each MSdata object within the MSslice is
## binned in the same bins.
mssB <- binRtime(mss, binSize=5)
mss
mssB
jotsetung/xcmsExtensions documentation built on May 19, 2019, 9:42 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Objects of the class Slots Extends Constructors and alike Accessing and subsetting Data visualizations Data manipulations Author(s) See Also Examples
Description
Sub-sets of an MS run across several samples can be stored in a
MSslice object. Such a slice of the MS data is defined by an
m/z and a retention time range in each sample. The actual data of the
slice in each sample is stored as MSdata object, i.e. as
intensities for each mz/rt tuple measured in a sample.
Depending on the measurements, the actual mz/rt ranges in each
individual MSdata can be slightly different, but all are
within the mz and rt range of the MSslice object (that can be
returned by the mzrange and rtrange method).
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 82 83 84 85 86 | ## S4 method for signature 'MSslice'
assayData(object)
## S4 replacement method for signature 'MSslice'
assayData(object) <- value
## S4 method for signature 'MSslice'
binMzRtime(object, FUN=max, mzNbin=NULL,
mzBinSize=NULL, rtNbin=NULL, rtBinSize=NULL)
## S4 method for signature 'MSslice'
binRtime(object, FUN=max, bins=NULL, nbin=NULL,
binSize=NULL)
## S4 method for signature 'MSslice'
getChromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, ...)
## S4 method for signature 'MSslice'
getSpectrum(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL, ...)
## S4 method for signature 'MSslice'
intrange(object)
## S4 method for signature 'MSslice'
length(x)
MSslice(x, ...)
## S4 method for signature 'MSslice'
msData(object, ...)
## S4 method for signature 'list'
msSlice(object, ...)
## S4 method for signature 'MSdata'
msSlice(object, ...)
## S4 method for signature 'xcmsSet'
msSlice(object, mzrange=NULL, rtrange=NULL,
rt="corrected", BPPARAM=MulticoreParam())
## S4 method for signature 'xcmsRaw'
msSlice(object, mzrange=NULL, rtrange=NULL, ...)
## S4 method for signature 'MSslice'
mzrange(object)
## S4 method for signature 'MSslice'
names(x)
## S4 replacement method for signature 'MSslice'
names(x) <- value
## S4 method for signature 'MSslice'
phenoData(object)
## S4 replacement method for signature 'MSslice'
phenoData(object) <- value
## S4 method for signature 'MSslice'
pData(object)
## S4 replacement method for signature 'MSslice'
pData(object) <- value
## S4 method for signature 'MSslice'
plotChromatogram(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL,
main=paste(format(mzrange(object), 2),
collapse="-"), xlab="Retention time",
ylab="Intensity", col=1, lty=1, ...)
## S4 method for signature 'MSslice'
plotSpectrum(object, FUN=max, bins=NULL,
nbin=NULL, binSize=NULL,
main=paste(format(rtrange(object), 2),
collapse="-"), xlab="M/Z",
ylab="Intensity", col=1, lty=1, ...)
## S4 method for signature 'MSslice'
rtrange(object)
## S4 method for signature 'MSslice'
subset(x, mzrange=NULL, rtrange=NULL)
|
Arguments
(in alphabetic order)
bins |
For |
binSize |
For |
FUN |
For |
BPPARAM |
Parallel processing parameters; see
|
col |
For |
lty |
For |
main |
For |
mzNbin |
For |
mzBinSize |
For |
mzrange |
A numeric vector defining the m/z-value range of the slice. |
nbin |
For |
object |
For For all other methods a |
rt |
For |
rtNbin |
For |
rtBinSize |
For |
rtrange |
A numeric vector defining the retention time range of the slice. |
value |
For For For For |
x |
For For |
xlab |
For |
ylab |
For |
... |
For For Ignored for all other methods. |
Value
Refer to the method and function description above for detailed information on the returned result object.
Objects of the class
While MSslice objects can be created by the constructor
function MSslice the default way to create such an object is by
using the msSlice method on an xcmsSet (or
xcmsRaw) object.
Slots
- assayData
-
A list of
MSdataobjects. - experimentData
-
Object of class
MIAPEcontaining details of experimental methods. - mzrange
-
A numeric vector of length 2 specifying the range of m/z values of the slice.
- phenoData
-
An
AnnoatedDataFrameproviding the sample description. - rtrange
-
A numeric vector of length 2 specifying the retention time range of the slice.
Extends
Class "Versioned" defined in the Biobase package, directly.
Constructors and alike
- MSslice
-
Constructor method to create a new
MSsliceinstance accepting either a list ofMSdataobjects or a singleMSdataobject. All additional arguments (e.g.phenoData,experimentData) are directly passed to the"new"call. - msSlice
-
Extract an
msSliceobject from anxcmsRaworxcmsSetobject. The latter (i.e. extraction from anxcmsSetobject) is the default constructor that will be mostly used. It allows to extract intensity values for the m/z and rt range that defines the slice of MS data from each individual sample. The result is returned as anMSsliceobject. If multiple mz and rt ranges are specified (i.e. argumentsmzrangeandrtrangeare 2-column matrices, each row specifying a different range) the result will be returned as anMSsliceListobject.Note that the
mzrangeandrtrangeof each of the extractedMSdatafor each sample will be slightly different, but all are within themzrangeandrtrangeof theMSsliceobject.If
objectis anMSdataobject it wraps that into anMSsliceobject.
Accessing and subsetting
- assayData,assayData<-
-
Get and set the assay data (i.e. the list of internal
MSdataobjects). This method is the same than themsDatamethod. - getChromatogram
-
Extracts a numeric matrix with the chromatogram (i.e. intensities along the retention time dimension) for each of the
MSdataobject and hence samples of theMSsliceobject. The rownames of the matrix represent the (unique) retention times and each column contains the spectrum of one sample/MSdataobject (i.e. the intensities aggregated in m/z direction for the respective retention time using the aggregation function specified with argumentFUN).In the default settings, without specifying any of the arguments
bins,nbinorbinSize, the method returns a matrix with one row for each unique retention time across all of the samples. Each row will only contain a numeric value for a sample in which a signal was measured for that specific retention time. In most instances it will be better to specifynbinorbinSize, to bin values also along the retention time dimension. Ideally, the binning should not be too coarse, but also not too detailed (in which case the matrix will again be relatively sparse); a binning with abinSize=1(i.e. one second), or slightly smaller, might be OK in most instances.For more details on the binning see the help for the
getChromatogrammethod ofMSdataobjects. - getSpectrum
-
Extracts a numeric matrix with the spectrum (i.e. intensities along the M/Z dimension) for each of the
MSdataobjects and hence samples of theMSsliceobject. The rownames of the matrix represent the distinct M/Z values and columns the individual samples. For more details (e.g. also on binning etc) see the help of thegetChromatogrammethod above. - intrange
-
Get the range of intensity values of the slice. This represents the range of values across all samples (i.e. all
MSdataobjects within theMSslice). Returns a numeric of length 2, orc(NA, NA)if the object is empty (or the internalMSdataobject(s) don't contain any data). - length
-
Get the length of the object, i.e. the number of
MSdataobject stored within the object. - msData
-
Get the
listofMSdataobjects. - mzrange
-
Get the m/z value range of the slice. This represents the range of values across all samples (i.e. all
MSdataobjects within theMSslice). Returns a numeric of length 2, orc(NA, NA)if the object is empty (or the internalMSdataobject(s) don't contain any data). - names,names<-
-
Get and set the names of the
MSdataobjects. - object[i]
-
Subsets the
MSsliceobject object and returns anMSsliceobject with only the elements selected byi.ican be an integer vector or a character vector, if names are available inobject. - object[[i]]
-
Extract e single
MSdataobject from theMSsliceobject. - phenoData,phenoData<-,pData,pData<-
-
Get and set the pheno data, i.e. the
AnnotatedDataFrameproviding the sample annotation (phenotypic information and covariates). Each row describing one sample each column representing one covariate. The ordering is assumed to be identical to the ordering of theMSdataobjects in theassayDataslot.The
pDatamethod accesses the same slot, but returns (and accepts) adata.frame. - rtrange
-
Get the retention time range of the slice. This represents the range of values across all samples (i.e. all
MSdataobjects within theMSslice). Returns a numeric of length 2, orc(NA, NA)if the object is empty (or the internalMSdataobject(s) don't contain any data). - subset
-
Subset the
MSslicebased on the specified M/Z and retention time ranges. The method returns aMSsliceobject.
Data visualizations
- plotChromatogram
-
Plots the chromatogram of the rt-m/z slice across all of the
MSdataobjects (i.e. samples). The argumentscolandltycan be used to use a different color for each line (i.e. sample) or a different line type. See description of thegetChromatogramfor details on the other parameters. - plotSpectrum
-
Plots the spectrum; see help of
plotChromatogramabove.
Data manipulations
- binMz
-
This method cuts the M/Z range of an
MSsliceobject 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
MSsliceobject. - 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
MSsliceobject 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
MSsliceobject.
Author(s)
Johannes Rainer.
See Also
xcmsSet, xcmsRaw,
MSdata, MSsliceList
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 | ## Load the faahKO package with the test data for the xcms package.
library(faahKO)
xset <- faahko
## Define a data sub-set and extract the corresponding values from
## the xcmsSet object. This will extract the intensity values of the
## defined slice from each individual sample.
rtr <- c(2600, 2670)
mzr <- c(300, 400)
mss <- msSlice(xset, rtrange=rtr, mzrange=mzr)
## Access the phenoData
phenoData(mss)
## Access individual columns using the $ method
mss$class
## Get the number of samples
length(mss)
## We don't have any names yet
names(mss)
## Setting the names using the ones provided by the sampnames method of the
## xcmsSet object.
names(mss) <- sampnames(xset)
names(mss)
## Subset to samples with name starting with wt
mssSub <- mss[grep(names(mss), pattern="^wt")]
names(mssSub)
## Extract a single MSdata object
mssSub[["wt18"]]
## Get the mz, rt and intensity range. This corresponds to the range of
## values of the slice across all samples.
mzrange(mss)
rtrange(mss)
intrange(mss)
## Extract the list of MSdata objects
msData(mss)
## Extract the chromatogram of a m/z-rt slice across all samples.
## Defining the mz and rt ranges for the peak in the xcms
## vignette (Figure 4).
mzr <- c(302, 302.5)
rtr <- c(2500, 2700)
mss <- msSlice(xset, rtrange=rtr, mzrange=mzr)
## We're getting a sparse matrix if we're not binning along the rt-dimension,
## since the retention times of the individual data points are slightly different
## between the samples:
head(getChromatogram(mss))
## We're next binning the values in retention time-bins of size 1 (1 second). By default
## (with FUN=max), the maximal signal is used for each bin.
chrM <- getChromatogram(mss, binSize=1)
dim(chrM)
head(chrM)
## We can also create an image from this matrix. Each column represents the chromatogram
## from one sample, each row one retention time bin with the intensity being color coded.
image(t(chrM))
## Next we plot the chromatogram of the slice across all samples.
## Without any binning:
plotChromatogram(mss, col="#00000080", type="l")
## And with binning.
plotChromatogram(mss, binSize=1, col="#00000080", type="l")
## Extracting the full MS data from the xcmsSet to create base peak chromatogram (BPC)
## and total ion chromatogram (TIC) plot of all samples.
msFull <- msSlice(xset)
## Base peak chromatogram with 1 second binning
plotChromatogram(msFull, binSize=1, col="#00000080", type="l")
## Total ion chromatogram with 1 second binning
plotChromatogram(msFull, FUN=sum, binSize=1, col="#00000080", type="l")
## Extending the M/Z range of the slice and extracting and plotting also the spectrum.
mzr <- c(300, 303)
mss <- msSlice(xset, rtrange=rtr, mzrange=mzr)
## Get the spectrum without binning:
head(getSpectrum(mss))
## We can also extract a slice from an xcmsRaw object, which will then
## contain the data only of that individual sample. Without specifying an
## mzrange and rtrange we extract the full data.
msSlice(getXcmsRaw(xset, 1))
par(mfrow=c(1, 2))
plotChromatogram(mss, binSize=1, col="#00000080", type="l")
plotSpectrum(mss, col="#00000040", type="h")
## Or from an MSdata object; extracting first a MSdata object containing
## the *full* MS data from a single file and creating then an MSslice object
## from that.
msd <- msData(getXcmsRaw(xset, 1))
msSlice(msd)
## Extracting the MSdata from the second sample and passing both to the
## MSslice constructor to generate a two-sample MSslice object.
msd2 <- msData(getXcmsRaw(xset, 2))
MSslice(list(msd, msd2))
####-------------
## Data manipulations
## We bin the MSslice object in 5 second retention time bins along the
## retention time dimension. Each MSdata object within the MSslice is
## binned in the same bins.
mssB <- binRtime(mss, binSize=5)
mss
mssB
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.