Preparation for the computational intensive peak filling step

cPrepFillChromPeaks, cGetChromPeakData, and cFillChromPeaks are small constructs of fillChromPeaks.

By running the functions as suggested in the vignette, we minimize the RAM usage, thus making the workflow scalable to tens of thousands of files.

Usage

cFillChromPeaksStep1(input, output, param, interval, settings)

Arguments

input

path to XcmsExperiment as returned by the peak alignment step

output

path(s) of the output file(s). This file goes into cFillChromPeaksStep2()

param

the object returned by xcms::FillChromPeaksParam()

interval

numeric vector of length 2 with start and end sample indices

settings

settings list from settings.yaml

Value

a list object with all the necessary objects for the cGetChromPeakData and cFillChromPeaks functions