DeconvoluteSpectrum {HiResTEC}

DeconvoluteSpectrum.

Description

DeconvoluteSpectrum will evaluate a list of xcmsRaw objects at a given time (rt) and potential mass (mz1). The main purpose is to deconvolute the mass spectrum at rt including mz1.

Usage

DeconvoluteSpectrum(
  dat = NULL,
  rt = NULL,
  rt_dev = 3,
  mz1 = NULL,
  mz_dev = 0.003,
  use.mz.adjust = FALSE,
  ionization = c("APCI", "ESI")[1],
  smooth = 0
)

Arguments

dat

A list of xcmsRaws or an xcmsSet object.

rt

Retention time to search for maxima.

rt_dev

Allowed retention time window.

mz1

If specified, ensure that this mass is included in the spectrum (assumed base peak). NULL otherwise.

mz_dev

Allowed mz deviation [Da].

use.mz.adjust

Will adjust mz on an experiment wide basis.

ionization

Either APCI or ESI. Choice will modify some internal parameters and checks performed.

smooth

Smoothing parameter passed on to getMultipleBPC.

Details

Will test all mz at spectrum of base peak within range for co-apex, rt diff and ratio consistency/correlation over a set of samples.

Value

A pseudo spectrum at rt (containing mz1 if specified). Effectively a 2-column matrix (mz, int) with rt as attribute

Examples

# Please use examples from previous versions as xcms (and xcms objects)
# are no longer supported during CRAN checks leading to package rejection
# if included (and I do not know a work around). :(