PreprocessingMSIData: Preprocessing of MSI data

In mridulaprasad/CorrDrugTumorMSI: A pipeline to combine drug distribution with tumor tissue-types in mass spectrometry imaging (MSI) data

Description

This function does peaks selection, removal of less frequent peaks and high intensity pixels from the tissue edge in MSI data.

For the peaks selection, first the adaptive bins are created based on maximum intenstiy reference spectrum from single or multiple MSI datasets. After bins creation, peaks selection performed from individual MSI dataset using local maxima search method. Threshold value to exclude the noisy peaks in the peaks selection step is automatically selected from ion-intensity region of the individual mass spectrum.

Usage

PreprocessingMSIData(folderpath, removePeaks = 0.2, edgecorrection = T)

Arguments

folderpath	path of MSI data folder. At the moment our function only supports the MSI data from in Analyze 7.5 format.
removePeaks	remove the bins from MSI data with lower coverage inside tissue below defined threshold
edgecorrection	remove high intensity pixels from the edge of the tissue. Logical operator with default value is T. If user does not want to perfom this action on their data then set to 'F'.

Value

two-dimensional matrix where total rows equal to total mass spectra in MSI data and total columns equal to bins created.

Examples

folderpath <- 'MSIdata//AVA-PTX'
PreprocessedMSIData <- PreprocessingMSIData(folderpath) # Does all default tasks:peaks selection, remove peaks with less coverage area and does edge correction
PreprocessedMSIData <- PreprocessingMSIData(folderpath, removePeaks=0.0) # Does peaks selection and edge correction. 
PreprocessedMSIData <- PreprocessingMSIData(folderpath,removePeaks=0.0,edgecorrection=F ) # Only peaks selection 
IonInensityMatrix   <- PreprocessedMSIData[[1]][[1]]
ycord               <- PreprocessedMSIData[[1]][[3]]; 
xcord               <- PreprocessedMSIData[[1]][[2]]; 
SingleionImage      <- IonInensityMatrix[,41]
dim(SingleionImage) <- c(ycord,xcord)
image(SingleionImage,axes=FALSE,col=rainbow(256))

mridulaprasad/CorrDrugTumorMSI documentation built on Oct. 26, 2020, 5:45 a.m.