deepblue_overlap {DeepBlueR} | R Documentation

## overlap

### Description

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.

### Usage

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

### Arguments

`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)

### 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_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`

### Examples

    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="%")

[Package DeepBlueR version 1.10.0 Index]