createKmerMotif {transite}R 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

createKmerMotif(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 <- createKmerMotif(
  "custom.motif", "RBP1",
  c("AAAAAAA", "CAAAAAA"), "HITS-CLIP",
  "Homo sapiens", "user"
)

[Package transite version 1.2.1 Index]