deepblue_flank {DeepBlueR}R Documentation

flank

Description

Create a set of genomic regions that flank the query regions. The original regions are removed from the query. Use the merge command to combine flanking regions with the original query.

Usage

deepblue_flank(query_id = NULL, start = NULL, length = NULL,
  use_strand = NULL, user_key = deepblue_options("user_key"))

Arguments

query_id

- A string (Query ID)

start

- A int (Number of base pairs after the end of the region. Use a negative number to denote the number of base pairs before the start of the region.)

length

- A int (The new region length)

use_strand

- A boolean (Use the region column STRAND to define the region direction)

user_key

- A string (users token key)

Value

id - A string (id of the new query)

See Also

Other Operating on the data regions: deepblue_aggregate, deepblue_binning, deepblue_count_regions, deepblue_coverage, deepblue_distinct_column_values, deepblue_extend, deepblue_filter_regions, deepblue_get_experiments_by_query, deepblue_get_regions, deepblue_input_regions, deepblue_intersection, deepblue_merge_queries, deepblue_overlap, deepblue_query_cache, deepblue_query_experiment_type, deepblue_score_matrix, deepblue_select_annotations, deepblue_select_experiments, deepblue_select_regions, deepblue_tiling_regions

Examples

annotation_id = deepblue_select_annotations(
    annotation_name="CpG Islands",
    genome="hg19", chromosome="chr1")
deepblue_flank(query_id = annotation_id,
    start = 0, length = 2000,
    use_strand = TRUE)


[Package DeepBlueR version 1.20.0 Index]