deepblue_find_motif {DeepBlueR}R Documentation

find_motif

Description

Find genomic regions based on a given motif that appears in the genomic sequence.

Usage

deepblue_find_motif(motif = NULL, genome = NULL, chromosomes = NULL,
  start = NULL, end = NULL, overlap = NULL,
  user_key = deepblue_options("user_key"))

Arguments

motif

- A string (motif (PERL regular expression))

genome

- A string (the target genome)

chromosomes

- A string or a vector of string (chromosome name(s))

start

- A int (minimum start region)

end

- A int (maximum end region)

overlap

- A boolean (if the matching should do overlap search)

user_key

- A string (users token key)

Value

id - A string (id of the annotation that contains the positions of the given motif)

See Also

Other Inserting and listing annotations: deepblue_list_annotations

Examples

deepblue_find_motif(motif = "C[GT]+C", chromosomes=c("chr11", "chr12"),
    genome = "hg19", overlap = FALSE)


[Package DeepBlueR version 1.19.1 Index]