annotSite               Annotate modification site
calculateProteolyticResistance
                        Calcutates proteolytic resistance for provided
                        data. Requires input from dataSummarizationLiP
                        function. Can optionally calculate differential
                        analysis using proteolytic resistance. In order
                        for this function to work, Conditions and run
                        numbers must match between the LiP and TrP
                        data.
calculateTrypticity     Calculates level of trypticity for a list of
                        LiP Peptides.
correlationPlotLiP      Plot run correlation for provided LiP and TrP
                        experiment.
dataProcessPlotsLiP     Visualization for explanatory data analysis
dataSummarizationLiP    Summarizes LiP and TrP datasets seperately
                        using methods from MSstats.
DIANNtoMSstatsLiPFormat
                        Converts raw LiP MS data from DIA-NN into the
                        format needed for MSstatsLiP.
groupComparisonLiP      Model LiP and TrP data and make adjustments if
                        needed Returns list of three modeled datasets
groupComparisonPlotsLiP
                        Visualization for model-based analysis and
                        summarization
LiPRawData              LiPRawData
locateMod               Locate modified sites with a peptide
locatePTM               Annotate modified sites with associated
                        peptides
MSstatsLiP_data         MSstatsLiP_data
MSstatsLiP_model        MSstatsLiP_model
MSstatsLiP_Summarized   MSstatsLiP_Summarized
PCAPlotLiP              Visualize PCA analysis for LiP and TrP
                        datasets.
raw_lip                 raw_lip
raw_prot                raw_prot
ResistanceBarcodePlotLiP
                        Proteolytic Resistance Barcode plot. Shows
                        accessibility score of different fully tryptic
                        peptides in a protein.
SkylineTest             SkylineTest
SkylinetoMSstatsLiPFormat
                        Converts raw LiP MS data from Skyline into the
                        format needed for MSstatsLiP.
SpectronauttoMSstatsLiPFormat
                        Converts raw LiP MS data from Spectronaut into
                        the format needed for MSstatsLiP.
StructuralBarcodePlotLiP
                        Barcode plot. Shows protein coverge of LiP
                        modified peptides.
tidyFasta               Read and tidy a FASTA file
TrPRawData              TrPRawData
trypticHistogramLiP     Histogram of Half vs Fully tryptic peptides.
                        Calculates proteotypicity, and then uses
                        calcualtions in histogram.
