SNP Effect Matrix (SEM) — SNPEffectMatrix-class • SEMPLR

A SNP Effect Matrix (SEM) estimates the binding affinity of every possible mutation in a particular transcription factor (TF) binding motif. Read more about SEMs here: https://doi.org/10.1093/bioinformatics/btz612 This class contains three slots: the matrix, the baseline value, and a unique id

Slots

sem: The 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)
baseline: A scrambled baseline, representing the binding score of randomly scrambled kmers of the same length. This is the binding cutoff for a TF
semId: basename of the sem file

Examples

# build a SEM example matrix
m <- matrix(rnorm(16), nrow = 4)
colnames(m) <- c("A", "C", "G", "T")

SNPEffectMatrix(sem = m, baseline = 1, semId = "sem_id")
#> An object of class SNPEffectMatrix
#> semId:  sem_id
#> baseline:  1
#> sem:
#>               A          C          G          T
#>           <num>      <num>      <num>      <num>
#> 1: -1.400043517  0.6215527 -0.2441996  2.0650249
#> 2:  0.255317055  1.1484116 -0.2827054 -1.6309894
#> 3: -2.437263611 -1.8218177 -0.5536994  0.5124269
#> 4: -0.005571287 -0.2473253  0.6289820 -1.8630115