Chromatogram-class: Representation of chromatographic MS data
In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description Usage Arguments Details Slots Author(s) See Also Examples

The Chromatogram class is designed to store chromatographic MS data, i.e. pairs of retention time and intensity values. Instances of the class can be created with the Chromatogram constructor function but in most cases the dedicated methods for OnDiskMSnExp and MSnExp objects extracting chromatograms should be used instead (i.e. the chromatogram method).

Chromatogram: create an instance of the Chromatogram class.

aggregationFun,aggregationFun<- get or set the aggregation function.

rtime returns the retention times for the rentention time - intensity pairs stored in the chromatogram.

intensity returns the intensity for the rentention time - intensity pairs stored in the chromatogram.

mz get the mz (range) of the chromatogram. The function returns a numeric(2) with the lower and upper mz value.

precursorMz get the mz of the precursor ion. The function returns a numeric(2) with the lower and upper mz value.

fromFile returns the value from the fromFile slot.

length returns the length (number of retention time - intensity pairs) of the chromatogram.

as.data.frame returns the rtime and intensity values from the object as data.frame.

filterRt: filters the chromatogram based on the provided retention time range.

clean: Removes unused 0-intensity data points. See clean documentation for more details and examples.

plot: plots a Chromatogram object.

msLevel returns the MS level of the chromatogram.

isEmpty returns TRUE for empty chromatogram or chromatograms with all intensities being NA.

productMz get the mz of the product chromatogram/ion. The function returns a numeric(2) with the lower and upper mz value.

bin aggregates intensity values from a chromatogram in discrete bins along the retention time axis and returns a Chromatogram object with the retention time representing the mid-point of the bins and the intensity the binned signal.

Chromatogram(
  rtime = numeric(),
  intensity = numeric(),
  mz = c(NA_real_, NA_real_),
  filterMz = c(NA_real_, NA_real_),
  precursorMz = c(NA_real_, NA_real_),
  productMz = c(NA_real_, NA_real_),
  fromFile = integer(),
  aggregationFun = character(),
  msLevel = 1L
)

aggregationFun(object)

## S4 method for signature 'Chromatogram'
show(object)

## S4 method for signature 'Chromatogram'
rtime(object)

## S4 method for signature 'Chromatogram'
intensity(object)

## S4 method for signature 'Chromatogram'
mz(object, filter = FALSE)

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

## S4 method for signature 'Chromatogram'
fromFile(object)

## S4 method for signature 'Chromatogram'
length(x)

## S4 method for signature 'Chromatogram'
as.data.frame(x)

## S4 method for signature 'Chromatogram'
filterRt(object, rt)

## S4 method for signature 'Chromatogram'
clean(object, all = FALSE, na.rm = FALSE)

## S4 method for signature 'Chromatogram,ANY'
plot(
  x,
  col = "#00000060",
  lty = 1,
  type = "l",
  xlab = "retention time",
  ylab = "intensity",
  main = NULL,
  ...
)

## S4 method for signature 'Chromatogram'
msLevel(object)

## S4 method for signature 'Chromatogram'
isEmpty(x)

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

## S4 method for signature 'Chromatogram'
bin(
  object,
  binSize = 0.5,
  breaks = seq(floor(min(rtime(object))), ceiling(max(rtime(object))), by = binSize),
  fun = max
)

`rtime`	`numeric` with the retention times (length has to be equal to the length of `intensity`).
`intensity`	`numeric` with the intensity values (length has to be equal to the length of `rtime`).
`mz`	`numeric(2)` representing the mz value range (min, max) on which the chromatogram was created. This is supposed to contain the real range of mz values in contrast to the `filterMz` below. If not applicable use `mzrange = c(0, 0)`.
`filterMz`	`numeric(2)` representing the mz value range (min, max) that was used to filter the original object on mz dimension. If not applicable use `filterMz = c(0, 0)`.
`precursorMz`	`numeric(2)` for SRM/MRM transitions. Represents the mz of the precursor ion. See details for more information.
`productMz`	`numeric(2)` for SRM/MRM transitions. Represents the mz of the product. See details for more information.
`fromFile`	`integer(1)` the index of the file within the `OnDiskMSnExp` or `MSnExp` from which the chromatogram was extracted.
`aggregationFun`	`character` string specifying the function that was used to aggregate intensity values for the same retention time across the mz range. Supported are `"sum"` (total ion chromatogram), `"max"` (base peak chromatogram), `"min"` and `"mean"`.
`msLevel`	`integer` with the MS level from which the chromatogram was extracted.
`object`	A `Chromatogram` object.
`filter`	For `mz`: whether the mz range used to filter the original object should be returned (`filter = TRUE`), or the mz range calculated on the real data (`filter = FALSE`).
`x`	For `as.data.frame` and `length`: a `Chromatogram` object.
`rt`	For `filterRt`: `numeric(2)` defining the lower and upper retention time for the filtering.
`all`	For `clean`: `logical(1)` whether all 0 intensities should be removed (default is `FALSE`). See `clean` for more details and examples.
`na.rm`	For `clean`: `logical(1)` whether all `NA` intensities should be removed before cleaning the `Chromatogram`. Defaults to `FALSE`. See `clean` for more details and examples.
`col`	For `plot`: the color to be used for plotting.
`lty`	For `plot`: the line type. See help page of `plot` in the `graphics` package for details.
`type`	For `plot`: the type of plot. See help page of `plot` in the `graphics` package for details.
`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.
`...`	For `plot`: additional arguments to be passed to the base 'plot' function.
`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`.
`fun`	for `bin`: function to be used to aggregate the intensity values falling within each bin.

The mz, filterMz, precursorMz and productMz are stored as a numeric(2) representing a range even if the chromatogram was generated for only a single ion (i.e. a single mz value). Using ranges for mz values allow this class to be used also for e.g. total ion chromatograms or base peak chromatograms.

The slots precursorMz and productMz allow to represent SRM (single reaction monitoring) and MRM (multiple SRM) chromatograms. As example, a Chromatogram for a SRM transition 273 -> 153 will have a @precursorMz = c(273, 273) and a @productMz = c(153, 153).

.__classVersion__,rtime,intensity,mz,filterMz,precursorMz,productMz,fromFile,aggregationFun,msLevel: See corresponding parameter above.

Johannes Rainer

MChromatograms for combining Chromatogram in a two-dimensional matrix (rows being mz-rt ranges, columns samples). chromatogram for the method to extract chromatogram data from a MSnExp or OnDiskMSnExp object. clean for the method to clean a Chromatogram object.

## Create a simple Chromatogram object.
ints <- abs(rnorm(100, sd = 100))
rts <- seq_len(length(ints))
chr <- Chromatogram(rtime = rts, intensity = ints)
chr

## Extract intensities
intensity(chr)

## Extract retention times
rtime(chr)

## Extract the mz range - is NA for the present example
mz(chr)

## plot the Chromatogram
plot(chr)

## Create a simple Chromatogram object based on random values.
chr <- Chromatogram(intensity = abs(rnorm(1000, mean = 2000, sd = 200)),
        rtime = sort(abs(rnorm(1000, mean = 10, sd = 5))))
chr

## Get the intensities
head(intensity(chr))

## Get the retention time
head(rtime(chr))

## What is the retention time range of the object?
range(rtime(chr))

## Filter the chromatogram to keep only values between 4 and 10 seconds
chr2 <- filterRt(chr, rt = c(4, 10))

range(rtime(chr2))