Access sems matrix from a SNPEffectMatrixCollection object

Usage

getSEMs(x, semId = NULL)

# S4 method for class 'SNPEffectMatrixCollection'
getSEMs(x, semId = NULL)

Arguments

x: SNPEffectMatrixCollection object
semId: optional character corresponding to an SEM in the SNPEffectMatrixCollection object. See semIds with names(getSEMs(x)). Defaults to returning all SEMs.

Value

A position (rows) by nucleic acid (columns) data.table is returned

Examples

## Create example SEM
df <- data.frame(
    A = c(1, 2, 3),
    C = c(1, 2, 3),
    G = c(1, 2, 3),
    T = c(1, 2, 3)
)
s <- SNPEffectMatrix(df, 1.205, "motif_id")
sc <- SNPEffectMatrixCollection(s)

## Access count matrix
getSEMs(sc)
#> $motif_id
#> An object of class SNPEffectMatrix
#> semId:  motif_id
#> baseline:  1.205
#> sem:
#>        A     C     G     T
#>    <num> <num> <num> <num>
#> 1:     1     1     1     1
#> 2:     2     2     2     2
#> 3:     3     3     3     3
#>