Create motif object

Create a Motif-class() object.

Usage

CreateMotifObject(
  data = NULL,
  pwm = NULL,
  motif.names = NULL,
  positions = NULL,
  meta.data = NULL
)

Arguments

data

A motif x region matrix

pwm

A named list of position weight matrices or position frequency matrices matching the motif names in data. Can be of class PFMatrixList.

motif.names

A named list of motif names. List element names must match the names given in pwm. If NULL, use the names from the list of position weight or position frequency matrices. This can be used to set a alternative common name for the motif. If a PFMatrixList is passed to pwm, it will pull the motif name from the PFMatrixList.

positions

A GenomicRanges::GRangesList() object containing exact positions of each motif.

meta.data

A data.frame containing metadata

Value

Returns a Motif-class() object

Examples

motif.matrix <- matrix(
  data = sample(c(0, 1),
    size = 100,
    replace = TRUE
  ),
  ncol = 5
)
rownames(motif.matrix) <- 1:nrow(motif.matrix)
motif <- CreateMotifObject(data = motif.matrix)