Package index • SEMplR

All functions

SEMC: Default SNP Effect Matrix Data Collection

SEMplScores(): SEMplScores object and constructor

SNPEffectMatrix-class: SNP Effect Matrix (SEM)

SNPEffectMatrix(): SNPEffectMatrix object and constructor

SNPEffectMatrixCollection-class: A collection of SNPEffectMatrix objects and their corresponding meta data

SNPEffectMatrixCollection(): SNPEffectMatrixCollection object and constructor

convertSEMsToPPMs(): Convert a SNP Effect Matrix to a position probability matrices (PPMs)

enrichSEMs(): Calculates binding enrichment for motif(s)

enrichmentSets(): Run the Full Differential‐Expression Motif Enrichment Pipeline

getBaseline(): Access baseline from a SNPEffectMatrix object

getCoordinates(): Retrieve Promoter Regions and Sample Background Elements

getRangeSeqs(): Get sequence for genomic ranges and variants

getRanges(): Access ranges slot in a SEMplScores object

getSEM(): Access the SEM from a SNPEffectMatrix object

getSEMId(): Access semId from a SNPEffectMatrix object

getSEMs(): Access sems matrix from a SNPEffectMatrixCollection object

loadSEMCollection(): Load .sem files and meta data into a SNPEffectMatrixCollection

mapIDs(): Map User IDs to Entrez and Determine Best Keytype

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

semData(): Accessor semData slot in a SEMplScores object

show(<SEMplScores>): Show method for SEMplScores objects

show(<SNPEffectMatrix>): Show for SNPEffectMatrix

show(<SNPEffectMatrixCollection>): Show method for SNPEffectMatrixCollection objects