deepblue_flank: flank
In MPIIComputationalEpigenetics/DeepBlue-R: DeepBlueR

Description Usage Arguments Value See Also Examples

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.

1 2	deepblue_flank(query_id = NULL, start = NULL, length = NULL, use_strand = NULL, user_key = deepblue_options("user_key"))

`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)

id - A string (id of the new query)

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

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)