Access semData from a SNPEffectMatrixCollection object

Access semData from a SNPEffectMatrixCollection object

Accessor semData slot in a SemplScores object

Usage

semData(x)

# S4 method for class 'SNPEffectMatrixCollection'
semData(x)

# S4 method for class 'SemplScores'
semData(x)

Arguments

x

a SemplScores object

Value

A 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))
sem_data <- data.frame(SEM = "motif_id", TF = "tf_id")
s <- SNPEffectMatrix(df, 1.205, "motif_id")
sc <- SNPEffectMatrixCollection(s, semData = sem_data, semKey = "SEM")

## Access count matrix
semData(sc)
#> Key: <SEM>
#>         SEM     TF
#>      <char> <char>
#> 1: motif_id  tf_id

library(VariantAnnotation)

# load default SEMs
data(sc)

# create a VRanges object
vr <- VRanges(seqnames = "chr12",
              ranges = 94136009, 
              ref = "G", alt = "C")

# calculate binding propensity
s <- scoreVariants(vr, sc, BSgenome.Hsapiens.UCSC.hg19::Hsapiens)

semData(s)
#> Key: <SEM>
#>         SEM     TF
#>      <char> <char>
#> 1: motif_id  tf_id