# Hierarchical Epitope pROtein biNding

## Documentation for package ‘HERON’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.HERONEpitopeDataSet | HERONEpitopeDataSet object and constructors
.HERONProbeDataSet | HERONProbeDataSet object and constructors
.HERONProteinDataSet | HERONProteinDataSet object and constructors
.HERONSequenceDataSet | 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
calcProbePValuesWUnpaired | Calculate Probe p-values using a two-sample wilcoxon 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
HERONEpitopeDataSet | HERONEpitopeDataSet object and constructors
HERONEpitopeDataSet-class | HERONEpitopeDataSet object and constructors
HERONProbeDataSet | HERONProbeDataSet object and constructors
HERONProbeDataSet-class | HERONProbeDataSet object and constructors
HERONProteinDataSet | HERONProteinDataSet object and constructors
HERONProteinDataSet-class | HERONProteinDataSet object and constructors
HERONSequenceDataSet | HERONSequenceDataSet object and constructors
HERONSequenceDataSet-class | HERONSequenceDataSet object and constructors
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