MassDataFrame-class {Cardinal} | R Documentation

## MassDataFrame: data frame with mass-to-charge ratio metadata

### Description

An `MassDataFrame` is an extension of the `XDataFrame` class with a special slot-column for observed mass-to-charge ratios.

### Usage

    MassDataFrame(mz, ..., row.names = NULL, check.names = TRUE)

### Arguments

`mz` | A `numeric` vector of mass-to-charge ratios.
`...` | Named arguments that will become columns of the object.
`row.names` | Row names to be assigned to the object; no row names are assigned if this is `NULL`.
`check.names` | Should the column names be checked for syntactic validity?

### Details

`MassDataFrame` is designed for mass spectrometry data. It includes a slot-column for the mass-to-charge ratio. It is intended to annotate either a single mass spectrum or an experiment where each mass spectrum share the same mass-to-charge ratios. The m/z values can be get and set by the `mz(object)` accessor, and are assumed to be unique and sorted in increasing order.

### Methods

`mz(object)`, `mz(object) <- value`:

  Get or set the mass-to-charge ratio slot-column.

`resolution(object)`, `resolution(object) <- value`:

  Get or set the estimated mass resolution of the mass-to-charge ratios. Typically, this should not be set manually.

`isCentroided(object)`:

  Guess whether the data are centroided or not, based on the m/z values.

`as.list(x, ..., slots = TRUE)`:

  Coerce the object to a `list`, where the slot-columns are included by default. Use `slots=FALSE` to exclude the slot-columns.

### Author(s)

Kylie A. Bemis

### See Also

`XDataFrame`

### Examples

    ## create an MassDataFrame object
    mz <- mz(from=200, to=220, by=200)
    values <- runif(length(mz))
    fdata <- MassDataFrame(mz=mz, values=values)

    ## check the mass-to-charge ratio properties
    head(mz(fdata))
    resolution(fdata)

[Package Cardinal version 2.6.0 Index]