getMultipleBPC: getMultipleBPC.

In HiResTEC: Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data

getMultipleBPC.

Description

getMultipleBPC will extract multiple BPCs from an xcmsRaw object for a vector of mz within the limits given by rt, rt_dev and mz_dev.

Usage

getMultipleBPC(
  x,
  mz = NULL,
  mz_dev = 0.005,
  rt = NULL,
  rt_dev = 2,
  zeroVal = NA,
  smooth = 0,
  returnEIC = FALSE
)

Arguments

x	xcmsRaw object.
mz	mass vector.
mz_dev	allowed deviations (can be a single numeric, a vector, a matrix with one row (lower bound, upper bound) or a matrix with length(mz) rows giving lower and upper bound for each mz).
rt	target timepoint.
rt_dev	allowed window.
zeroVal	Set values <=0 to NA or keep as is with NULL.
smooth	Window size for moving average smoother, 0 = no smoothing.
returnEIC	Return EIC instead of BPC?

Details

While there are other functions to extract BPC information from raw data, this one is particularly useful to get all traces belonging to a isotopologue group. It will attach several derived values to the results object, i.e. describing the observed mass shift (deviation from expected value) which is helpful in QC for non-targeted tracer analyses.

Value

A matrix with scan wise (rows) intensities for all requested masses (columns) as either EIC or BPC.

References

Uses C code modified from XCMS (see citation("xcms")).

Examples

# see \link{plotMID} for an example

HiResTEC documentation built on March 7, 2023, 5:47 p.m.