xcms (version 1.48.0)

profRange-methods: 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

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(), ...)

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.

See Also

xcmsRaw-class