deepblue_export_bed {DeepBlueR} | R Documentation |
Export GenomicRanges result as BED file
deepblue_export_bed(result, target.directory = "./", file.name, score.field = NULL)
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) |
return value of write.table
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")