getMultipleBPC {HiResTEC}

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 or NULL (default) to return the TIC.

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 time point or NULL (default) to use full scan time.

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{plotBPC} for an example