Chromatograms-class {MSnbase} | R Documentation |
The Chromatograms
class allows to store
Chromatogram
objects in a matrix
-like
two-dimensional structure.
Chromatograms
: create an instance of class
Chromatograms
.
Chromatograms
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 Chromatograms
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 NAnnotatedDataFrame
object.
pData
: accesses the phenotypical description of the
samples. Returns a data.frame
.
pData<-
: replace the phenotype data.
$
and $<-
: get or replace individual columns of
the object's pheno data.
colnames<-
: replace or set the column names of the
Chromatograms
object. Does also set the rownames
of the
phenoData
.
sampleNames
: get the sample names.
sampleNames<-
: replace or set the sample names of the
Chromatograms
object (i.e. the rownames
of the pheno data
and colnames
of the data matrix.
isEmpty
: returns TRUE
if the Chromatograms
object or all of its Chromatogram
objects is/are empty or contain
only NA
intensities.
Chromatograms(data, phenoData, ...) ## S4 method for signature 'Chromatograms' show(object) ## S4 method for signature 'Chromatograms,ANY,ANY,ANY' x[i, j, drop = FALSE] ## S4 replacement method for signature 'Chromatograms' x[i, j] <- value ## S4 method for signature 'Chromatograms,ANY' plot(x, col = "#00000060", lty = 1, type = "l", xlab = "retention time", ylab = "intensity", main = NULL, ...) ## S4 method for signature 'Chromatograms' phenoData(object) ## S4 method for signature 'Chromatograms' pData(object) ## S4 replacement method for signature 'Chromatograms,data.frame' pData(object) <- value ## S4 method for signature 'Chromatograms' x$name ## S4 replacement method for signature 'Chromatograms' x$name <- value ## S4 replacement method for signature 'Chromatograms' colnames(x) <- value ## S4 method for signature 'Chromatograms' sampleNames(object) ## S4 replacement method for signature 'Chromatograms,ANY' sampleNames(object) <- value ## S4 method for signature 'Chromatograms' isEmpty(x)
data |
A |
phenoData |
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 |
The Chromatograms
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
mz 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.
For [
: the subset of the Chromatograms
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 Chromatograms
object is returned. If drop = TRUE
is specified, the method
returns a list
of Chromatogram
objects.
For phenoData
: an NAnnotatedDataFrame
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.
Subsetting with [
will always return a Chromatograms
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.
Johannes Rainer
Chromatogram
for the class representing chromatogram
data.
chromatogram
for the method to extract a
Chromatograms
object from a MSnExp
or
OnDiskMSnExp
object.
## Creating some chromatogram objects to put them into a Chromatograms 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 Chromatograms object with 2 rows and 2 columns chrs <- Chromatograms(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 Chromatograms ## 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 ## 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 Chromatograms object chrs <- Chromatograms(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"))