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
Source:R/AllClasses.R, R/methods-SNPEffectMatrix.R
SNPEffectMatrix-class.Rdhttps://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
show for SNPEffectMatrix
Usage
# S4 method for class 'SNPEffectMatrix'
show(object)Slots
semThe SEM itself as a data table Rows represent sequence position (variable length), columns represent effects due to each nucleotide base A, C, G, T (fixed length: 4)
baselineA scrambled baseline, representing the binding score of randomly scrambled kmers of the same length. This is the binding cutoff for a TF
semIdbasename of the sem file