Prepare data to plot overlap between datatable of SNPs and cell-type-specific epigenomic peaks and coaccessibility data. — CORCES2020_prepare_bulkATAC_peak_overlap • echoannot

Prepare data to plot overlap between datatable of SNPs and cell-type-specific epigenomic peaks and coaccessibility data.

CORCES2020_prepare_bulkATAC_peak_overlap(
  merged_DT,
  FDR_filter = NULL,
  snp_filter = "Consensus_SNP==TRUE",
  add_HiChIP_FitHiChIP = TRUE,
  annotate_genes = FALSE,
  return_counts = TRUE,
  verbose = TRUE
)

Source

https://doi.org/10.1038/s41588-020-00721-x

See also

Other CORCES2020: CORCES2020_get_ATAC_peak_overlap(), CORCES2020_get_hichip_fithichip_overlap(), CORCES2020_prepare_scATAC_peak_overlap(), get_CORCES2020_bulkATACseq_peaks(), get_CORCES2020_cicero_coaccessibility(), get_CORCES2020_hichip_fithichip_loop_calls(), get_CORCES2020_scATACseq_celltype_peaks(), get_CORCES2020_scATACseq_peaks()

Examples

if (FALSE) {
dat_melt <- echoannot:::CORCES2020_prepare_bulkATAC_peak_overlap(
    merged_DT = echodata::get_Nalls2019_merged()
)
}