profRange-methods {xcms} | R Documentation

## Specify a subset of profile mode data

### Description

Specify a subset of the profile mode matrix given a mass, time, or scan range. Allow flexible user entry for other functions.

### Arguments

`object` | the `xcmsRaw` object
`mzrange` | single numeric mass or vector of masses
`rtrange` | single numeric time (in seconds) or vector of times
`scanrange` | single integer scan index or vector of indecies
`...` | arguments to other functions

### Details

This function handles selection of mass/time subsets of the profile matrix for other functions. It allows the user to specify such subsets in a variety of flexible ways with minimal typing.

Because R does partial argument matching, `mzrange`, `scanrange`, and `rtrange` can be specified in short form using `m=`, `s=`, and `t=`, respectively. If both a `scanrange` and `rtrange` are specified, then the `rtrange` specification takes precedence.

When specifying ranges, you may either enter a single number or a numeric vector. If a single number is entered, then the closest single scan or mass value is selected. If a vector is entered, then the range is set to the `range()` of the values entered. That allows specification of ranges using shortened, slightly non-standard syntax. For example, one could specify 400 to 500 seconds using any of the following: `t=c(400,500)`, `t=c(500,400)`, or `t=400:500`. Use of the sequence operator (`:`) can save several keystrokes when specifying ranges. However, while the sequence operator works well for specifying integer ranges, fractional ranges do not always work as well.

### Value

A list with the folloing items:

`mzrange` | numeric vector with start and end mass
`masslab` | textual label of mass range
`massidx` | integer vector of mass indecies
`scanrange` | integer vector with stat ane end scans
`scanlab` | textual label of scan range
`scanidx` | integer vector of scan range
`rtrange` | numeric vector of start and end times
`timelab` | textual label of time range

### Methods

object = "xcmsRaw"

  `profRange(object, mzrange = numeric(), rtrange = numeric(), scanrange = numeric(), ...)`

### See Also

`xcmsRaw-class`

[Package xcms version 3.0.2 Index]