deepblue_get_regions: get_regions

Description Usage Arguments Value See Also Examples

Description

Trigger the processing of the query's genomic regions. The output is a column based format with columns as defined in the 'output_format' parameter. Use the command 'info' for verifying the processing status. The 'get_request_data' command is used to download the regions using the programmatic interface. Alternatively, results can be download using the URL: http://deepblue.mpi-inf.mpg.de/download?r_id=<request_id>&key=<user_key>.

Usage

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deepblue_get_regions(query_id = NULL, output_format = NULL,
  user_key = deepblue_options("user_key"))

Arguments

query_id

- A string (Query ID)

output_format

- A string (Output format)

user_key

- A string (users token key)

Value

request_id - A string (Request ID - Use it to retrieve the result with info() and get_request_data())

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_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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data_id = deepblue_select_experiments(
    experiment_name="E002-H3K9ac.narrowPeak.bed")
deepblue_get_regions(query_id =data_id,
    output_format = "CHROMOSOME,START,END")

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