SNP Effect Matrix Pipeline in R

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Documentation for package ‘SEMPLR’ version 0.99.2

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

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