HERONEpitopeDataSet-class
                        HERONEpitopeDataSet object and constructors
HERONProbeDataSet-class
                        HERONProbeDataSet object and constructors
HERONProteinDataSet-class
                        HERONProteinDataSet object and constructors
HERONSequenceDataSet-class
                        HERONSequenceDataSet object and constructors
addSequenceAnnotations
                        Add Sequence Annotations for Epitopes
calcCombPValues         Calculate p-values using the "exprs" assay
calcEpitopePValues      Calculate epitope-level p-values
calcProbePValuesTPaired
                        Calculate Probe p-values using a differential
                        paired t-test
calcProbePValuesTUnpaired
                        Calculate Probe p-values using a differential
                        unpaired t-test
calcProteinPValues      Calculate protein-level p-values
catSequences            Concatenate sequences together based upon their
                        start positions. Assumes the probe sequences
                        have an overlap.
convertSequenceDSToProbeDS
                        Convert HERONSequenceDataSet to
                        HERONProbeDataSet
findBlocksProbeT        Find Blocks of consecutive probes
findBlocksT             Find consecutive probes
findEpitopeSegments     Find Epitopes from probe stats and calls.
getEpitopeID            Create EpitopeID from protein, first and last
                        probes
getEpitopeIDsToProbeIDs
                        Get probe ids from a vector of epitope ids
getEpitopeProbeIDs      Get the vector of probes from an epitope id
getEpitopeProtein       Obtain Protein Id from Epitope ID
getEpitopeStart         Obtain first probe's protein start position
                        from Epitope ID
getEpitopeStop          Obtain last probe's protein start position from
                        EpitopeID
getKofN                 Get K of N statistics from an experiment with
                        padj and calls
getProteinLabel         Get Protein Label from Probe
getProteinStart         Get the amino-acid starting position of the
                        probe within the protein.
getProteinTiling        Get Protein Tiling
heffron2021_wuhan       SARS CoV-2 Wuhan Peptide Binding Array Data
log2Transform           log2 transform the "exprs" assay
makeEpitopeCalls        Make Epitope Calls
makeProbeCalls          Making Probe-level Calls
makeProteinCalls        Make Protein-level Calls
min_max                 Cap vector at minimum/maximum values
oneHitEpitopes          Find One-hit epitopes
oneHitProbes            Find one hit probes
oneProbeEpitopes        Indicate which epitopes are just one probe.
probeHitSupported       Find probe hits with a consecutive probe or
                        another sample
pvalue_to_zscore        Convert p-value matrix to a z-score matrix
quantileNormalize       Normalize the exprs assay using quantile
                        normalization
smoothProbeDS           Smooth probes across protein tiling
