deepblue_flank: flank

Description Usage Arguments Value See Also Examples

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

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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

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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)

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