profRange-methods: Specify a subset of profile mode data

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.