deepblue_aggregate: aggregate

Description Usage Arguments Value See Also Examples

Description

Summarize the data_id content using the regions specified in ranges_id as boundaries. Use the fields @AGG.MIN, @AGG.MAX, @AGG.SUM, @AGG.MEDIAN, @AGG.MEAN, @AGG.VAR, @AGG.SD, @AGG.COUNT in 'get_regions' command 'format' parameter to retrieve the computed values minimum, maximum, median, mean, variance, standard deviation and number of regions, respectively.

Usage

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deepblue_aggregate(data_id = NULL, ranges_id = NULL, column = NULL,
  user_key = deepblue_options("user_key"))

Arguments

data_id

- A string (id of the query with the data)

ranges_id

- A string (id of the query with the regions range)

column

- A string (name of the column that will be used in the aggregation)

user_key

- A string (users token key)

Value

regions - A string (query id of this aggregation operation)

See Also

Other Operating on the data regions: 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_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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annotation_id = deepblue_select_annotations(
    annotation_name="CpG Islands",
    genome="hg19", chromosome="chr1")
data_id = deepblue_select_experiments(
    experiment_name="E002-H3K9ac.narrowPeak.bed")
deepblue_aggregate(
    data_id = data_id,
    ranges_id=annotation_id,
    column = "SCORE")

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