deepblue_export_bed: Export GenomicRanges result as BED file

In MPIIComputationalEpigenetics/DeepBlue-R: DeepBlueR

Description

Export GenomicRanges result as BED file

Usage

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

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/DeepBlue-R documentation built on Aug. 11, 2021, 3:18 p.m.