deepblue_overlap: overlap
In MPIIComputationalEpigenetics/DeepBlue-R: DeepBlueR

Description Usage Arguments Value See Also Examples

Select genomic regions that overlap or not overlap with with the specified number of regions of the second query. Important: This command is still experimental and changes may occour.

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deepblue_overlap(query_data_id = NULL, query_filter_id = NULL,
  overlap = NULL, amount = NULL, amount_type = NULL,
  user_key = deepblue_options("user_key"))

`query_data_id`	- A string (query data that will be filtered.)
`query_filter_id`	- A string (query containing the regions that the regions of the query_data_id must overlap.)
`overlap`	- A boolean (True if must overlap, or false if must not overlap.)
`amount`	- A int (Amount of regions that must overlap. Use the parameter 'amount_type' ('bp' or '%') to specify the unit. For example, use the value '10' with the amount_type '%' to specify that 10% of the bases in both regions must overlap, or use '10' with the amount_type 'bp' to specify that at least 10 bases must or must not overlap.)
`amount_type`	- A string (Type of the amount: 'bp' for base pairs and '%' for percentage. )
`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_flank, deepblue_get_experiments_by_query, deepblue_get_regions, deepblue_input_regions, deepblue_intersection, deepblue_merge_queries, 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")
experiment_id = deepblue_select_experiments(
    experiment_name="S00XDKH1.ERX712765.H3K27ac.bwa.GRCh38.20150527.bed")
deepblue_overlap(query_data_id = experiment_id, query_filter_id = annotation_id, 
    overlap = TRUE, amount=10, amount_type="%")