deepblue_export_bed: Export GenomicRanges result as BED file

Description Usage Arguments Value Examples

Description

Export GenomicRanges result as BED file

Usage

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deepblue_export_bed(result, target.directory = "./", file.name,
  score.field = NULL)

Arguments

result

A result from a DeepBlue request such as a set of genomic regions.

target.directory

The directory to save the file to

file.name

The name of the file without suffix

score.field

Which column of the results should be used to populate the score column of the BED file (optional)

Value

return value of write.table

Examples

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query_id = deepblue_select_experiments (
experiment=c("GC_T14_10.CPG_methylation_calls.bs_call.GRCh38.20160531.wig"),
chromosome="chr1", start=0, end=50000000)
cpg_islands = deepblue_select_annotations(annotation_name="CpG Islands",
genome="GRCh38", chromosome="chr1", start=0, end=50000000)
overlapped = deepblue_aggregate (data_id=query_id, ranges_id=cpg_islands,
                                column="VALUE" )
request_id = deepblue_get_regions(query_id=overlapped,
                                output_format=
                                     "CHROMOSOME,START,END,@AGG.MIN,@AGG.MAX,@AGG.MEAN,@AGG.VAR")
regions = deepblue_download_request_data(request_id=request_id)
temp_dir = tempdir()
deepblue_export_bed(regions, target.directory = temp_dir,
                  file.name = "GC_T14_10.CpG_islands")

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