deepblue_export_bed {DeepBlueR}R Documentation

Export GenomicRanges result as BED file

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")

[Package DeepBlueR version 1.19.1 Index]