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