PeakList2PeakMatrix: PeakList2PeakMatrix.

In prafols/rMSIproc: MSI Processing in C++

Description

Convert's an R peak list into a peak matrix.

Usage

PeakList2PeakMatrix(
  PeakList,
  PosMatrix,
  BinTolerance = 5,
  BinToleranceUsingPPM = T,
  BinFilter = 0.1,
  imgUUID = rMSI:::uuid_timebased(),
  imgName = "rMSIproc_PeakList2PeakMatrix_peakMat"
)

Arguments

PeakList	R peak list. Missing values will be set to zero.
PosMatrix	the pos matrix as following the same format as in rMSI object.
BinTolerance	tolerance used to merge peaks to the same bin. It is recomanded to use the half of peak width in ppm units.
BinToleranceUsingPPM	if True the peak binning tolerance is specified in ppm, if false the tolerance is set using scans.
BinFilter	the peaks bins non detected in at least the BinFitler*TotalNumberOfPixels spectra will be deleted.
imgUUID	a unique ID for the peak matrix, if not provided it will be automatically generated.
imgName	the name of the original MSI dataset.

Value

peak matrix.

Examples

 
  #Import an imzML using centroid mode (after peak picking).
  pkLst <- rMSIproc::import_imzMLpeakList("~/path/to/processed/data/file.imzML")
  
  #Run the peak-binning to get the peak matrix.
  myPkMat <- rMSIproc::PeakList2PeakMatrix(pkLst$peakList, pkLst$pos, BinTolerance = 25, BinToleranceUsingPPM = T)
  
  #Save the peak matrix. 
  rMSIproc::StorePeakMatrix("~/path/to/file.zip", myPkMat)

prafols/rMSIproc documentation built on Dec. 12, 2021, 7:31 p.m.