create_matrix_motif: Creates Transite motif object from position weight matrix

In kkrismer/transite: RNA-binding protein motif analysis

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

create_matrix_motif(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 <- create_matrix_motif(
  "custom_motif", "RBP1",
  transite:::toy_motif_matrix, "HITS-CLIP",
  "Homo sapiens", "user"
)

kkrismer/transite documentation built on Feb. 9, 2024, 3:23 a.m.