CORCES2020_prepare_scATAC_peak_overlap: Prepare CORCES2020 scATAC-seq peak overlap data

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

Prepare CORCES2020 scATAC-seq peak overlap data

Description

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

Usage

CORCES2020_prepare_scATAC_peak_overlap(
  merged_DT,
  FDR_filter = NULL,
  snp_filter = "Consensus_SNP==TRUE",
  add_cicero = TRUE,
  annotate_genes = TRUE,
  return_counts = TRUE,
  verbose = TRUE
)

Source

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

merged_DT <- echodata::get_Nalls2019_merged() dat_melt <- echoannot:::CORCES2020_prepare_scATAC_peak_overlap( merged_DT = merged_DT)

See Also

Other CORCES2020: CORCES2020_get_ATAC_peak_overlap(), CORCES2020_get_hichip_fithichip_overlap(), CORCES2020_prepare_bulkATAC_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()

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.