CORCES2020_get_ATAC_peak_overlap: Get overlap between datatable of SNPs and scATAC peaks

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

Get overlap between datatable of SNPs and scATAC peaks

Description

Can optionally add Cicero coaccessibility scores, which are also derived from scATAC-seq data.

Usage

CORCES2020_get_ATAC_peak_overlap(
  query_dat,
  FDR_filter = NULL,
  add_cicero = TRUE,
  cell_type_specific = TRUE,
  verbose = TRUE
)

Arguments

query_dat	Genomic summary statistics data to query with.
FDR_filter	Correct p-value threshold.
add_cicero	Whether to include cicero results as well.
cell_type_specific	Whether to use bulk or cell-type-specific data.
verbose	Print messages.

Source

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

See Also

Other CORCES2020: CORCES2020_get_hichip_fithichip_overlap(), CORCES2020_prepare_bulkATAC_peak_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

query_dat <- echodata::BST1[1:100,]
gr.hits <- echoannot::CORCES2020_get_ATAC_peak_overlap(query_dat = query_dat)

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