Looking at groups only: Compute the fraction of 3D-peak pair groups per Raw file which have an acceptable RT difference after alignment using the result from 'idTransferCheck()', i.e. compute the fraction of groups which are within a certain RT tolerance.
A data.frame with columns 'fc.raw.file', 'rtdiff_mixed', 'rtdiff_genuine'
The allowed matching difference for each Raw file (as data.frame(fc.rawfile, m))
Returned value is between 0 (bad) and 1 (all within tolerance).
A data.frame with one row for each raw.file and columns 'raw.file' and score 'withinRT' (0-1)
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