deepblue_enrich_regions_overlap {DeepBlueR} | R Documentation

## enrich_regions_overlap

### Description

Enrich the regions based on regions overlap analysis.

### Usage

    deepblue_enrich_regions_overlap(query_id = NULL, background_query_id = NULL,
      datasets = NULL, genome = NULL, user_key = deepblue_options("user_key"))

### Arguments

`query_id` | - A string (Query ID)
`background_query_id` | - A string (query_id containing the regions that will be used as the background data.)
`datasets` | - A struct (a map where each key is an identifier and the value is a list containing experiment names or query_ids (you can use both together).)
`genome` | - A string (the target genome)
`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(). The result is a list containing the datasets that overlap with the query_id regions.)

### See Also

Other Enrich the genome regions: `deepblue_enrich_regions_fast`, `deepblue_enrich_regions_go_terms`

### Examples

    query_id = deepblue_select_experiments(
      experiment_name="S00VEQA1.hypo_meth.bs_call.GRCh38.20150707.bed")

    filtered_query_id = deepblue_filter_regions(
      query_id = query_id,
      field = "AVG_METHYL_LEVEL",
      operation = "<",
      value = "0.0025",
      type="number")

    rg_10kb_tilling = deepblue_tiling_regions(
        size = 1000,
        genome = "hg19")

    # We could have included more Epigenetic Marks here
    epigenetic_marks <- c("h3k27ac", "H3K27me3", "H3K4me3")

    histones_datasets = c()
    for (i in 1:length(epigenetic_marks)) {
      experiments_list <- deepblue_list_experiments(
        epigenetic_mark=epigenetic_marks[[i]],
        type="peaks",
        genome="grch38",
        project="BLUEPRINT Epigenome");

        experiment_names = deepblue_extract_names(experiments_list)
        histones_datasets[[epigenetic_marks[[i]]]] = experiment_names
    }

    deepblue_enrich_regions_overlap(
      query_id=filtered_query_id,
      background_query=rg_10kb_tilling,
      datasets=histones_datasets,
      genome="grch38")

[Package DeepBlueR version 1.12.0 Index]