Get overlap between datatable of SNPs and scATAC peaks — CORCES2020_get_ATAC_peak_overlap • echoannot

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

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

Source

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

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.

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)
#> CORCES2020:: Extracting overlapping cell-type-specific scATAC-seq peaks
#> Converting dat to GRanges object.
#> 1 query SNP(s) detected with reference overlap.
#> + CORCES2020:: No Cicero hits found.