create_kmer_motif: Creates Transite motif object from character vector of...

View source: R/misc.R

create_kmer_motifR Documentation

Creates Transite motif object from character vector of k-mers

Description

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

Usage

create_kmer_motif(id, rbps, kmers, 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

kmers

character vector of k-mers that are associated with the motif, set of k-mers is valid if (1) all k-mers must have the same length, (2) only hexamers or heptamers allowed, (3) allowed characters are A, C, G, U

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_kmer_motif(
  "custom_motif", "RBP1",
  c("AAAAAAA", "CAAAAAA"), "HITS-CLIP",
  "Homo sapiens", "user"
)

kkrismer/transite documentation built on July 13, 2024, 8:01 a.m.