removeMatrix_padded_new: Remove Matrix Padded New

In gbaquer3/rMSIcleanup: Anotation and removal of the matrix peaks in MALDI data

Remove Matrix Padded New

Description

Remove the matrix following the method presented by Fonville et al. 2012. It takes a padded image where there is a wide enough region of pixels outside of the tissue. It consists of three basic steps.

Usage

removeMatrix_padded_new(
  pks,
  normalize = TRUE,
  matrix_cor = 0.65,
  tissue_cor = 0.6,
  exo_method = 1,
  max_exo = 10
)

Arguments

pks	Peak Matrix
normalize	Boolean value to determine if normalization is to be performed. If TRUE TIC normalization is performed
matrix_cor	Correlation threshold over which a given peak is considered to be a matrix peak
tissue_cor	Correlation threshold under which a given peak is considered to be a tissue peak
exo_method	Method to determine the reference matrix peaks
max_exo	Number of peaks used as base for the correlation

Value

List of mass indices considered to be endogenous. The rest of the peaks are deamed as matrix related or non-anatomically relevant.

gbaquer3/rMSIcleanup documentation built on Feb. 24, 2023, 2:58 p.m.