To run the analysis, run RunAnalysis.sh , what follows is a description of some of the files

input_manually_refined.csv is the input to use for MSStats, it was taken from the three separate skyline outputs provided by Veronika (in the seaprate folder)
it was manually fixed to
-- remove the standardtype column
-- rename the ratiotoglobalstandard column to intensity
-- remove the control peptides
-- remove the RPA4 protein which is not interesting to us
-- add in NA values for bio-rep 6 for proteins BLM NUCL TRIM28 and H2AX
   -- biorep 6 wasn't analyzed, so I added one fake run, for bio rep 6 with all NA transitions for each peptide of each of these proteins

run the refiner on input manually fixed, generate refined, then do the R analysis
the refiner now also multiplies all intensities by 10,000(or something like that) to make it so no intensities are less than 1
