createMatrixMotif {transite}R Documentation

Creates Transite motif object from position weight matrix

Description

Takes a position weight matrix (PWM) and meta info and returns an object of class RBPMotif.

Usage

createMatrixMotif(id, rbps, matrix, type, species, src)

Arguments

id

motif id (character vector of length 1)

rbps

character vector of names of RNA-binding proteins associated with this motif

matrix

data frame with four columns (A, C, G, U) and 6 - 15 rows (positions), where cell (i, j) contains weight of nucleotide j on position i

type

type of motif (e.g., 'HITS-CLIP', 'EMSA', 'SELEX', etc.)

species

species where motif was discovered (e.g., 'Homo sapiens')

src

source of motif (e.g., 'RBPDB v1.3.1')

Value

object of class RBPMotif

Examples

custom.motif <- createMatrixMotif(
  "custom.motif", "RBP1",
  transite:::toy.motif.matrix, "HITS-CLIP",
  "Homo sapiens", "user"
)

[Package transite version 1.2.1 Index]