# SNP Effect Matrix Pipeline in R

## Documentation for package ‘SEMPLR’ version 1.0.1

- 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