Package index
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show(<SNPEffectMatrix>) - https://doi.org/10.1093/bioinformatics/btz612 A SNP Effect Matrix (SEM) estimates the binding affinity of every possible mutation in a particular transcription factor (TF) binding motif This class contains three slots: the matrix, the baseline value, and a unique id
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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 variants
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SemplScores() - SemplScores object and constructor
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SequenceFrame-class - Class to store information about sequencing frame and variant location
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SequenceFrame() - SequenceFrame object and constructor
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baseline() - Access baseline from a SNPEffectMatrix object
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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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getFlankingSeqs() - Get up and downstream sequences of variant(s) and store in VRanges metadata
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loadSEM() - Load matrix and baseline data from .sem files
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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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querySeqs() - Get up and downstream sequences of a variant
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sc - Default SNP Effect Matrix Data Collection
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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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sem() - Access sem matrix from a SNPEffectMatrix object
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semData() - Access semData from a SNPEffectMatrixCollection object
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semId() - Access semId from a SNPEffectMatrix object
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sems() - Access sems matrix from a SNPEffectMatrixCollection object
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show(<SNPEffectMatrixCollection>)show(<SemplScores>)show(<SequenceFrame>) - Show method for SNPEffectMatrixCollection objects
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variants() - Accessor variants slot in a SemplScores object
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viewFrames() - View the top scoring frames for a given variant and SEM