deepblue_find_motif: find_motif

In MPIIComputationalEpigenetics/DeepBlue-R: DeepBlueR

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)

MPIIComputationalEpigenetics/DeepBlue-R documentation built on Aug. 11, 2021, 3:18 p.m.