SNPEffectMatrix object and constructor

Constructs a SNPEffectMatrix class object.

Usage

SNPEffectMatrix(sem, baseline, semId)

Arguments

sem

A data.table object of format base position (rows) by nucleic acid (columns). Column names must inclue A, C, T, and G; other columns will be ignored.

baseline

A numeric scrambled baseline, representing the binding score of randomly scrambled kmers of the same length.

semId

A character unique identifier for the SEM.

Value

a SNPEffectMatrix object

Examples

# build a matrix for a motif of length 4
m <- matrix(rnorm(16), nrow = 4)
colnames(m) <- c("A", "C", "G", "T")

# build a SNPEffectMatrix object
SNPEffectMatrix(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: -0.9140748  0.7377763 -0.01595031 0.1764886
#> 2:  0.4681544  1.8885049 -0.82678895 0.2436855
#> 3:  0.3629513 -0.0974451 -1.51239965 1.6235489
#> 4: -1.3045435 -0.9358474  0.93536319 0.1120381