MChromatograms-class: Container for multiple Chromatogram objects
In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics
Description
Usage
Arguments
Details
Value
Note
Author(s)
See Also
Examples
Description
The MChromatograms class allows to store
Chromatogram objects in a matrix-like
two-dimensional structure.
MChromatograms: create an instance of class
MChromatograms.
MChromatograms objects can, just like a matrix,
be subsetted using the [ method. Single elements, rows or columns
can be replaced using e.g. x[1, 1] <- value where value
has to be a Chromatogram object or a list of such objects.
plot: plots a MChromatograms object. For each row
in the object one plot is created, i.e. all Chromatogram
objects in the same row are added to the same plot.
phenoData: accesses the phenotypical desccription of the
samples. Returns an AnnotatedDataFrame object.
pData: accesses the phenotypical description of the
samples. Returns a data.frame.
pData<-: replace the phenotype data.
$ and $<-: get or replace individual columns of
the object's pheno data.
colnames<-: replace or set the column names of the
MChromatograms object. Does also set the rownames of the
phenoData.
sampleNames: get the sample names.
sampleNames<-: replace or set the sample names of the
MChromatograms object (i.e. the rownames of the pheno data
and colnames of the data matrix.
isEmpty: returns TRUE if the MChromatograms
object or all of its Chromatogram objects is/are empty or contain
only NA intensities.
featureNames: returns the feature names of the
MChromatograms object.
featureNames<-: set the feature names.
featureData: return the feature data.
featureData<-: replace the object's feature data.
fData: return the feature data as a data.frame.
fData<-: replace the object's feature data by passing a
data.frame
fvarLabels: return the feature data variable names (i.e.
column names).
rownames<-: replace the rownames (and featureNames) of
the object.
precursorMz: return the precursor m/z from the chromatograms. The
method returns a matrix with 2 columns ("mzmin" and
"mzmax") and as many rows as there are rows in the
MChromatograms object. Each row contains the precursor m/z of the
chromatograms in that row. An error is thrown if the chromatograms within one
row have different precursor m/z values.
productMz: return the product m/z from the chromatograms. The
method returns a matrix with 2 columns ("mzmin" and
"mzmax") and as many rows as there are rows in the
MChromatograms object. Each row contains the product m/z of the
chromatograms in that row. An error is thrown if the chromatograms within one
row have different product m/z values.
mz: returns the m/z for each row of the MChromatograms object
as a two-column matrix (with columns "mzmin" and
"mzmax").
polarity: returns the polarity of the scans/chromatograms: '1',
'0' or '-1' for positive, negative or unknown polarity.
bin aggregates intensity values of chromatograms in discrete bins
along the retention time axis. By default, individual Chromatogram
objects of one row are binned into the same bins. The function returns a
MChromatograms object with binned chromatograms.
clean: removes 0-intensity data points. Either all of them
(with all = TRUE) or all except those adjacent to non-zero
intensities (all = FALSE; default). See clean
documentation for more details and examples.
Usage
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MChromatograms(data, phenoData, featureData, ...)
## S4 method for signature 'MChromatograms'
show(object)
## S4 method for signature 'MChromatograms,ANY,ANY,ANY'
x[i, j, drop = FALSE]
## S4 replacement method for signature 'MChromatograms'
x[i, j] <- value
## S4 method for signature 'MChromatograms,ANY'
plot(
x,
col = "#00000060",
lty = 1,
type = "l",
xlab = "retention time",
ylab = "intensity",
main = NULL,
...
)
## S4 method for signature 'MChromatograms'
phenoData(object)
## S4 method for signature 'MChromatograms'
pData(object)
## S4 replacement method for signature 'MChromatograms,data.frame'
pData(object) <- value
## S4 method for signature 'MChromatograms'
x$name
## S4 replacement method for signature 'MChromatograms'
x$name <- value
## S4 replacement method for signature 'MChromatograms'
colnames(x) <- value
## S4 method for signature 'MChromatograms'
sampleNames(object)
## S4 replacement method for signature 'MChromatograms,ANY'
sampleNames(object) <- value
## S4 method for signature 'MChromatograms'
isEmpty(x)
## S4 method for signature 'MChromatograms'
featureNames(object)
## S4 replacement method for signature 'MChromatograms'
featureNames(object) <- value
## S4 method for signature 'MChromatograms'
featureData(object)
## S4 replacement method for signature 'MChromatograms,ANY'
featureData(object) <- value
## S4 method for signature 'MChromatograms'
fData(object)
## S4 replacement method for signature 'MChromatograms,ANY'
fData(object) <- value
## S4 method for signature 'MChromatograms'
fvarLabels(object)
## S4 replacement method for signature 'MChromatograms'
rownames(x) <- value
## S4 method for signature 'MChromatograms'
precursorMz(object)
## S4 method for signature 'MChromatograms'
productMz(object)
## S4 method for signature 'MChromatograms'
mz(object)
## S4 method for signature 'MChromatograms'
polarity(object)
## S4 method for signature 'MChromatograms'
bin(object, binSize = 0.5, breaks = numeric(), fun = max)
## S4 method for signature 'MChromatograms'
clean(object, all = FALSE, na.rm = FALSE)
Arguments
data
A list of Chromatogram objects.
phenoData
either a data.frame, AnnotatedDataFrame or
AnnotatedDataFrame describing the phenotypical information of the
samples.
featureData
either a data.frame or AnnotatedDataFrame
with additional information for each row of chromatograms.
...
Additional parameters to be passed to the
matrix constructor, such as nrow, ncol
and byrow.
object
a MChromatograms object.
x
For all methods: a MChromatograms object.
i
For [: numeric, logical or character
defining which row(s) to extract.
j
For [: numeric, logical or character
defining which columns(s) to extract.
drop
For [: logical(1) whether to drop the
dimensionality of the returned object (if possible). The default is
drop = FALSE, i.e. each subsetting returns a MChromatograms
object (or a Chromatogram object if a single element is
extracted).
value
For [<-: the replacement object(s). Can be a list
of Chromatogram objects or, if length of i and
j are 1, a single Chromatogram object.
For pData<-: a data.frame with the number of rows matching
the number of columns of object.
For colnames: a character with the new column names.
col
For plot: the color to be used for plotting. Either a
vector of length 1 or equal to ncol(x).
lty
For plot: the line type (see plot in the
graphics package
for more details. Can be either a vector of length 1 or of length equal
to ncol(x).
type
For plot: the type of plot (see
plot from the graphics package for more details.
Can be either a vector
of length 1 or of length equal to ncol(x).
xlab
For plot: the x-axis label.
ylab
For plot: the y-axis label.
main
For plot: the plot title. If not provided the mz range
will be used as plot title.
name
For $, the name of the pheno data column.
binSize
for bin: numeric(1) with the size of the bins
(in seconds).
breaks
for bin: numeric defining the bins. Usually not
required as the function calculates the bins automatically based on
binSize and the retention time range of chromatograms in the same
row.
fun
for bin: function to be used to aggregate the intensity
values falling within each bin.
all
for clean: logical(1) whether all 0 intensities
should be removed (all = TRUE), or whether 0-intensities
adjacent to peaks should be kept (all = FALSE; default).
na.rm
for clean: logical(1) whether all NA
intensities should be removed prior to clean 0 intensity data points.
Details
The MChromatograms class extends the base matrix class
and hence allows to store Chromatogram objects in a
two-dimensional array. Each row is supposed to contain
Chromatogram objects for one MS data slice with a common
m/z and rt range. Columns contain Chromatogram objects from the
same sample.
plot: if nrow(x) > 1 the plot area is split into
nrow(x) sub-plots and the chromatograms of one row are plotted in
each.
Value
For [: the subset of the MChromatograms object. If a
single element is extracted (e.g. if i and j are of length
1) a Chromatogram object is returned. Otherwise (if
drop = FALSE, the default, is specified) a MChromatograms
object is returned. If drop = TRUE is specified, the method
returns a list of Chromatogram objects.
For phenoData: an AnnotatedDataFrame representing the
pheno data of the object.
For pData: a data.frame representing the pheno data of
the object.
For $: the value of the corresponding column in the pheno data
table of the object.
Note
Subsetting with [ will always return a MChromatograms
object (with the exception of extracting a single element)
unless drop = TRUE is specified. This is different from the
default subsetting behaviour of matrix-like objects.
Author(s)
Johannes Rainer
See Also
Chromatogram for the class representing chromatogram
data.
chromatogram for the method to extract a
MChromatograms object from a MSnExp or
OnDiskMSnExp object.
readSRMData for the function to read chromatographic data
of an SRM/MRM experiment.
Examples
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## Creating some chromatogram objects to put them into a MChromatograms object
ints <- abs(rnorm(25, sd = 200))
ch1 <- Chromatogram(rtime = 1:length(ints), ints)
ints <- abs(rnorm(32, sd = 90))
ch2 <- Chromatogram(rtime = 1:length(ints), ints)
ints <- abs(rnorm(19, sd = 120))
ch3 <- Chromatogram(rtime = 1:length(ints), ints)
ints <- abs(rnorm(21, sd = 40))
ch4 <- Chromatogram(rtime = 1:length(ints), ints)
## Create a MChromatograms object with 2 rows and 2 columns
chrs <- MChromatograms(list(ch1, ch2, ch3, ch4), nrow = 2)
chrs
## Extract the first element from the second column. Extracting a single
## element always returns a Chromatogram object.
chrs[1, 2]
## Extract the second row. Extracting a row or column (i.e. multiple elements
## returns by default a list of Chromatogram objects.
chrs[2, ]
## Extract the second row with drop = FALSE, i.e. return a MChromatograms
## object.
chrs[2, , drop = FALSE]
## Replace the first element.
chrs[1, 1] <- ch3
chrs
## Add a pheno data.
pd <- data.frame(name = c("first sample", "second sample"),
idx = 1:2)
pData(chrs) <- pd
## Column names correspond to the row names of the pheno data
chrs
## Access a column within the pheno data
chrs$name
## Access the m/z ratio for each row; this will be NA for the present
## object
mz(chrs)
## Create some random Chromatogram objects
ints <- abs(rnorm(123, mean = 200, sd = 32))
ch1 <- Chromatogram(rtime = seq_along(ints), intensity = ints, mz = 231)
ints <- abs(rnorm(122, mean = 250, sd = 43))
ch2 <- Chromatogram(rtime = seq_along(ints), intensity = ints, mz = 231)
ints <- abs(rnorm(125, mean = 590, sd = 120))
ch3 <- Chromatogram(rtime = seq_along(ints), intensity = ints, mz = 542)
ints <- abs(rnorm(124, mean = 1200, sd = 509))
ch4 <- Chromatogram(rtime = seq_along(ints), intensity = ints, mz = 542)
## Combine into a 2x2 MChromatograms object
chrs <- MChromatograms(list(ch1, ch2, ch3, ch4), byrow = TRUE, ncol = 2)
## Plot the second row
plot(chrs[2, , drop = FALSE])
## Plot all chromatograms
plot(chrs, col = c("#ff000080", "#00ff0080"))
MSnbase documentation built on Jan. 23, 2021, 2 a.m.
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Description Usage Arguments Details Value Note Author(s) See Also Examples
Description
The MChromatograms class allows to store
Chromatogram objects in a matrix-like
two-dimensional structure.
MChromatograms: create an instance of class
MChromatograms.
MChromatograms objects can, just like a matrix,
be subsetted using the [ method. Single elements, rows or columns
can be replaced using e.g. x[1, 1] <- value where value
has to be a Chromatogram object or a list of such objects.
plot: plots a MChromatograms object. For each row
in the object one plot is created, i.e. all Chromatogram
objects in the same row are added to the same plot.
phenoData: accesses the phenotypical desccription of the
samples. Returns an AnnotatedDataFrame object.
pData: accesses the phenotypical description of the
samples. Returns a data.frame.
pData<-: replace the phenotype data.
$ and $<-: get or replace individual columns of
the object's pheno data.
colnames<-: replace or set the column names of the
MChromatograms object. Does also set the rownames of the
phenoData.
sampleNames: get the sample names.
sampleNames<-: replace or set the sample names of the
MChromatograms object (i.e. the rownames of the pheno data
and colnames of the data matrix.
isEmpty: returns TRUE if the MChromatograms
object or all of its Chromatogram objects is/are empty or contain
only NA intensities.
featureNames: returns the feature names of the
MChromatograms object.
featureNames<-: set the feature names.
featureData: return the feature data.
featureData<-: replace the object's feature data.
fData: return the feature data as a data.frame.
fData<-: replace the object's feature data by passing a
data.frame
fvarLabels: return the feature data variable names (i.e.
column names).
rownames<-: replace the rownames (and featureNames) of
the object.
precursorMz: return the precursor m/z from the chromatograms. The
method returns a matrix with 2 columns ("mzmin" and
"mzmax") and as many rows as there are rows in the
MChromatograms object. Each row contains the precursor m/z of the
chromatograms in that row. An error is thrown if the chromatograms within one
row have different precursor m/z values.
productMz: return the product m/z from the chromatograms. The
method returns a matrix with 2 columns ("mzmin" and
"mzmax") and as many rows as there are rows in the
MChromatograms object. Each row contains the product m/z of the
chromatograms in that row. An error is thrown if the chromatograms within one
row have different product m/z values.
mz: returns the m/z for each row of the MChromatograms object
as a two-column matrix (with columns "mzmin" and
"mzmax").
polarity: returns the polarity of the scans/chromatograms: '1',
'0' or '-1' for positive, negative or unknown polarity.
bin aggregates intensity values of chromatograms in discrete bins
along the retention time axis. By default, individual Chromatogram
objects of one row are binned into the same bins. The function returns a
MChromatograms object with binned chromatograms.
clean: removes 0-intensity data points. Either all of them
(with all = TRUE) or all except those adjacent to non-zero
intensities (all = FALSE; default). See clean
documentation for more details and examples.
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 87 88 89 90 91 | MChromatograms(data, phenoData, featureData, ...)
## S4 method for signature 'MChromatograms'
show(object)
## S4 method for signature 'MChromatograms,ANY,ANY,ANY'
x[i, j, drop = FALSE]
## S4 replacement method for signature 'MChromatograms'
x[i, j] <- value
## S4 method for signature 'MChromatograms,ANY'
plot(
x,
col = "#00000060",
lty = 1,
type = "l",
xlab = "retention time",
ylab = "intensity",
main = NULL,
...
)
## S4 method for signature 'MChromatograms'
phenoData(object)
## S4 method for signature 'MChromatograms'
pData(object)
## S4 replacement method for signature 'MChromatograms,data.frame'
pData(object) <- value
## S4 method for signature 'MChromatograms'
x$name
## S4 replacement method for signature 'MChromatograms'
x$name <- value
## S4 replacement method for signature 'MChromatograms'
colnames(x) <- value
## S4 method for signature 'MChromatograms'
sampleNames(object)
## S4 replacement method for signature 'MChromatograms,ANY'
sampleNames(object) <- value
## S4 method for signature 'MChromatograms'
isEmpty(x)
## S4 method for signature 'MChromatograms'
featureNames(object)
## S4 replacement method for signature 'MChromatograms'
featureNames(object) <- value
## S4 method for signature 'MChromatograms'
featureData(object)
## S4 replacement method for signature 'MChromatograms,ANY'
featureData(object) <- value
## S4 method for signature 'MChromatograms'
fData(object)
## S4 replacement method for signature 'MChromatograms,ANY'
fData(object) <- value
## S4 method for signature 'MChromatograms'
fvarLabels(object)
## S4 replacement method for signature 'MChromatograms'
rownames(x) <- value
## S4 method for signature 'MChromatograms'
precursorMz(object)
## S4 method for signature 'MChromatograms'
productMz(object)
## S4 method for signature 'MChromatograms'
mz(object)
## S4 method for signature 'MChromatograms'
polarity(object)
## S4 method for signature 'MChromatograms'
bin(object, binSize = 0.5, breaks = numeric(), fun = max)
## S4 method for signature 'MChromatograms'
clean(object, all = FALSE, na.rm = FALSE)
|
Arguments
data |
A |
phenoData |
either a |
featureData |
either a |
... |
Additional parameters to be passed to the
|
object |
a |
x |
For all methods: a |
i |
For |
j |
For |
drop |
For |
value |
For For For |
col |
For |
lty |
For |
type |
For |
xlab |
For |
ylab |
For |
main |
For |
name |
For |
binSize |
for |
breaks |
for |
fun |
for |
all |
for |
na.rm |
for |
Details
The MChromatograms class extends the base matrix class
and hence allows to store Chromatogram objects in a
two-dimensional array. Each row is supposed to contain
Chromatogram objects for one MS data slice with a common
m/z and rt range. Columns contain Chromatogram objects from the
same sample.
plot: if nrow(x) > 1 the plot area is split into
nrow(x) sub-plots and the chromatograms of one row are plotted in
each.
Value
For [: the subset of the MChromatograms object. If a
single element is extracted (e.g. if i and j are of length
1) a Chromatogram object is returned. Otherwise (if
drop = FALSE, the default, is specified) a MChromatograms
object is returned. If drop = TRUE is specified, the method
returns a list of Chromatogram objects.
For phenoData: an AnnotatedDataFrame representing the
pheno data of the object.
For pData: a data.frame representing the pheno data of
the object.
For $: the value of the corresponding column in the pheno data
table of the object.
Note
Subsetting with [ will always return a MChromatograms
object (with the exception of extracting a single element)
unless drop = TRUE is specified. This is different from the
default subsetting behaviour of matrix-like objects.
Author(s)
Johannes Rainer
See Also
Chromatogram for the class representing chromatogram
data.
chromatogram for the method to extract a
MChromatograms object from a MSnExp or
OnDiskMSnExp object.
readSRMData for the function to read chromatographic data
of an SRM/MRM experiment.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | ## Creating some chromatogram objects to put them into a MChromatograms object
ints <- abs(rnorm(25, sd = 200))
ch1 <- Chromatogram(rtime = 1:length(ints), ints)
ints <- abs(rnorm(32, sd = 90))
ch2 <- Chromatogram(rtime = 1:length(ints), ints)
ints <- abs(rnorm(19, sd = 120))
ch3 <- Chromatogram(rtime = 1:length(ints), ints)
ints <- abs(rnorm(21, sd = 40))
ch4 <- Chromatogram(rtime = 1:length(ints), ints)
## Create a MChromatograms object with 2 rows and 2 columns
chrs <- MChromatograms(list(ch1, ch2, ch3, ch4), nrow = 2)
chrs
## Extract the first element from the second column. Extracting a single
## element always returns a Chromatogram object.
chrs[1, 2]
## Extract the second row. Extracting a row or column (i.e. multiple elements
## returns by default a list of Chromatogram objects.
chrs[2, ]
## Extract the second row with drop = FALSE, i.e. return a MChromatograms
## object.
chrs[2, , drop = FALSE]
## Replace the first element.
chrs[1, 1] <- ch3
chrs
## Add a pheno data.
pd <- data.frame(name = c("first sample", "second sample"),
idx = 1:2)
pData(chrs) <- pd
## Column names correspond to the row names of the pheno data
chrs
## Access a column within the pheno data
chrs$name
## Access the m/z ratio for each row; this will be NA for the present
## object
mz(chrs)
## Create some random Chromatogram objects
ints <- abs(rnorm(123, mean = 200, sd = 32))
ch1 <- Chromatogram(rtime = seq_along(ints), intensity = ints, mz = 231)
ints <- abs(rnorm(122, mean = 250, sd = 43))
ch2 <- Chromatogram(rtime = seq_along(ints), intensity = ints, mz = 231)
ints <- abs(rnorm(125, mean = 590, sd = 120))
ch3 <- Chromatogram(rtime = seq_along(ints), intensity = ints, mz = 542)
ints <- abs(rnorm(124, mean = 1200, sd = 509))
ch4 <- Chromatogram(rtime = seq_along(ints), intensity = ints, mz = 542)
## Combine into a 2x2 MChromatograms object
chrs <- MChromatograms(list(ch1, ch2, ch3, ch4), byrow = TRUE, ncol = 2)
## Plot the second row
plot(chrs[2, , drop = FALSE])
## Plot all chromatograms
plot(chrs, col = c("#ff000080", "#00ff0080"))
|
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