SNPEffectMatrixCollection object and constructor

Constructs a SNPEffectMatrixCollection class object.

Usage

SNPEffectMatrixCollection(sems, semData = NULL, semKey = "")

Arguments

sems

A list of SNPEffectMatrix objects

semData

A data.table containing meta data for each SEM

semKey

A column name in semData corresponding to the semIds in each SNPEffectMatrix object in the sems parameter

Value

a SNPEffectMatrixCollection object

Examples

# 
# build two matries for a motif of length 4
m1 <- matrix(rnorm(16), nrow = 4)
m2 <- matrix(rnorm(16), nrow = 4)
colnames(m1) <- c("A", "C", "G", "T")
colnames(m2) <- c("A", "C", "G", "T")

# build two SNPEffectMatrix objects
s1 <- SNPEffectMatrix(m1, baseline = 1, semId = "sem_id_1")
s2 <- SNPEffectMatrix(m2, baseline = 1, semId = "sem_id_2")

# build a meta data table
md <- data.table::data.table(transcription_factor = c("tf1", "tf2"), 
                             cell_type = c("HepG2", "K562"), 
                             sem_id = c("sem_id_1", "sem_id_2"))

# build a SNPEffectMatrixCollection object
SNPEffectMatrixCollection(list(s1, s2), semData = md, semKey = "sem_id")
#> Updating semKey to 'SEM_KEY'.
#> An object of class SNPEffectMatrixCollection
#> sems(2): sem_id_1, sem_id_2
#> semData(4): transcription_factor, cell_type, sem_id, SEM_KEY