Chromatograms-class {MSnbase}R Documentation

Container for multiple Chromatogram objects

Description

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 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 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.

featureNames: returns the feature names of the Chromatograms 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 Chromatograms 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 Chromatograms 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 Chromatograms 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 Chromatograms 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

Chromatograms(data, phenoData, featureData, ...)

## 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)

## S4 method for signature 'Chromatograms'
featureNames(object)

## S4 replacement method for signature 'Chromatograms'
featureNames(object) <- value

## S4 method for signature 'Chromatograms'
featureData(object)

## S4 replacement method for signature 'Chromatograms,ANY'
featureData(object) <- value

## S4 method for signature 'Chromatograms'
fData(object)

## S4 replacement method for signature 'Chromatograms,ANY'
fData(object) <- value

## S4 method for signature 'Chromatograms'
fvarLabels(object)

## S4 replacement method for signature 'Chromatograms'
rownames(x) <- value

## S4 method for signature 'Chromatograms'
precursorMz(object)

## S4 method for signature 'Chromatograms'
productMz(object)

## S4 method for signature 'Chromatograms'
mz(object)

## S4 method for signature 'Chromatograms'
polarity(object)

## S4 method for signature 'Chromatograms'
bin(object, binSize = 0.5,
  breaks = numeric(), fun = max)

## S4 method for signature 'Chromatograms'
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 Chromatograms object.

x

For all methods: a Chromatograms 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 Chromatograms 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 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 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 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 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 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 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 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.

Author(s)

Johannes Rainer

See Also

Chromatogram for the class representing chromatogram data. chromatogram for the method to extract a Chromatograms object from a MSnExp or OnDiskMSnExp object. readSRMData for the function to read chromatographic data of an SRM/MRM experiment.

Examples

## 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

## 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 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"))
[Package MSnbase version 2.12.0 Index]