NormalizeByAcqDegradationOnTargetPeaks: NormalizeByAcqDegradationOnTargetPeaks: Calculates the...

In prafols/rMSI: MSI Tools

Description

NormalizeByAcqDegradationOnTargetPeaks: Calculates the normalization of each pixel as the sum of areas of specified peaks. Each normalization coeficient is smoothed by its neighbours to compensate for ionization degradation during acqusition.

Usage

NormalizeByAcqDegradationOnTargetPeaks(
  img,
  mz_vector,
  mz_window_size = 0.1,
  norm_name = "AcqSelPK",
  winSize = 0.1
)

Arguments

img	the rMSI image object.
mz_vector	a vector containing m/z values of peaks to be used for normalization.
mz_window_size	specifies the with of peak gaussian. Set to 0.1 Da by default which is OK for reflector TOF MALDI instrument
norm_name	a name to be used for the normalization. Default is set to "SelPK".
winSize	the window size use for smoothing (0 to 1).

Value

a rMSI image containing the normalizations$<name> field

prafols/rMSI documentation built on Dec. 12, 2021, 7:29 p.m.