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 1.8.1 Index]