Package index
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SEMC - Default SNP Effect Matrix Data Collection
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SEMplScores() - SEMplScores object and constructor
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SNPEffectMatrix-class - SNP Effect Matrix (SEM)
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SNPEffectMatrix() - SNPEffectMatrix object and constructor
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SNPEffectMatrixCollection-class - A collection of SNPEffectMatrix objects and their corresponding meta data
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SNPEffectMatrixCollection() - SNPEffectMatrixCollection object and constructor
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SEMplScores-class - Class for storing SEM motif binding calculations for multiple genomic ranges or variants
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convertSEMsToPPMs() - Convert a SNP Effect Matrix to a position probability matrices (PPMs)
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enrichSEMs() - Calculates binding enrichment for motif(s)
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getBaseline() - Access baseline from a SNPEffectMatrix object
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getRangeSeqs() - Get sequence for genomic ranges and variants
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getRanges() - Access ranges slot in a SEMplScores object
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getSEM() - Access the SEM from a SNPEffectMatrix object
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getSEMId() - Access semId from a SNPEffectMatrix object
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getSEMs() - Access sems matrix from a SNPEffectMatrixCollection object
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loadSEMCollection() - Load .sem files and meta data into a SNPEffectMatrixCollection
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plotEnrich() - Plot the results of
enrichSEMs
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plotSEM() - Plot SEM scores for each nucleic acid in each position of the motif
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plotSEMMotifs() - Plot non-alt versus alt binding propensity for a single variant
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plotSEMVariants() - Plot non-alt versus alt binding propensity for a single motif
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scoreBinding() - Calculate binding propensity for all SEM motifs and genomic positions provided
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scoreVariants() - Calculate risk/non-risk binding propensity for all SEM motifs and variants provided
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semData() - Accessor semData slot in a SEMplScores object
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show(<SEMplScores>) - Show method for SEMplScores objects
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show(<SNPEffectMatrix>) - Show for SNPEffectMatrix
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show(<SNPEffectMatrixCollection>) - Show method for SNPEffectMatrixCollection objects