process_ABC: Process ABC scores and save as a GRanges object

In kevinlkx/Mapgen: Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Process ABC scores and save as a GRanges object

Description

Process ABC scores and save as a GRanges object

Usage

process_ABC(
  ABC,
  gene.annots = NULL,
  full.element = FALSE,
  score.thresh = 0.015,
  flank = 0
)

Arguments

ABC	A data frame of ABC scores from Nasser et al. Nature 2021 paper
gene.annots	If provided, restrict to genes in gene.annots
full.element	Logical; if TRUE, use full length of ABC elements extracted from the "name" column. Otherwise, use the original (narrow) regions provided in the ABC scores data.
score.thresh	Numeric. Threshold of ABC scores. (default = 0.015, as in Nasser et al. Nature 2021 paper).
flank	Integer. Extend bases on both sides of the ABC elements (default = 0).

Value

a GRanges object with processed ABC scores, with genomic coordinates of the interacting regions and gene names (promoters).

kevinlkx/Mapgen documentation built on April 2, 2024, 5:48 a.m.