Hierarchical Epitope pROtein biNding

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Documentation for package ‘HERON’ version 1.4.0

• 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