Check SNP-annotation overlap for GoShifter — GOSHIFTER_check_overlap • echoannot

Determine which annotation BED regions overlap with the SNPs in the GoShifter snpmap file.

GOSHIFTER_check_overlap(output_bed, GS_results_path, overlap_threshold = 1)

Arguments

output_bed: Path to the annotation BED file.
GS_results_path: Path to the GoShifter results directory (must contain snpmap.txt).
overlap_threshold: Minimum overlaps required (not actively filtered here; used for reference only).

Value

A data.table of BED regions overlapping with the SNPs.

See also

Other GOSHIFTER: GOSHIFTER(), GOSHIFTER_bed_names(), GOSHIFTER_create_LD(), GOSHIFTER_create_snpmap(), GOSHIFTER_find_folder(), GOSHIFTER_get_roadmap_annotations(), GOSHIFTER_heatmap(), GOSHIFTER_histograms_SNPgroups(), GOSHIFTER_histograms_pvals(), GOSHIFTER_list_chromatin_states(), GOSHIFTER_process_results(), GOSHIFTER_run(), GOSHIFTER_search_ROADMAP(), GOSHIFTER_summarise_results()