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.
1 2 3 | 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
1 2 3 4 5 6 7 | 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="%")
|
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