deepblue_find_motif: find_motif

Description Usage Arguments Value See Also Examples

Description

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

Usage

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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

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

MPIIComputationalEpigenetics/DeepBlueR documentation built on May 8, 2019, 3:19 p.m.