find_peaks_near_genes: Find peaks or regions near gene body or TSS

In quadbiolab/Pando: Inferring regulomes from multi-modal single-cell genomics data

Find peaks or regions near gene body or TSS

Description

Find peaks or regions near gene body or TSS

Usage

find_peaks_near_genes(
  peaks,
  genes,
  sep = c("-", "-"),
  method = c("Signac", "GREAT"),
  upstream = 1e+05,
  downstream = 0,
  extend = 1e+06,
  only_tss = FALSE,
  verbose = TRUE
)

Arguments

peaks	A GRanges object with peak regions.
sep	Vector of separators to use for genomic string. First element is used to separate chromosome and coordinates, second separator is used to separate start and end coordinates.
upstream	Integer defining the distance upstream of the gene/TSS to consider.
downstream	Integer defining the distance downstream of the gene/TSS to consider.
extend	Integer defining the distance from the upstream and downstream of the basal regulatory region. Used only when method is 'GREAT'.
only_tss	Logical. Measure distance from the TSS (TRUE) or from the entire gene body (FALSE).
verbose	Logical. Display messages
gene	A GRanges object with gene coordinates.
methos	Character specifying the method to link peak overlapping motif regions to nearby genes. On of 'Signac' or 'GREAT'.

Value

A sparse binary Matrix with gene/peak matches.

quadbiolab/Pando documentation built on April 22, 2024, 8:14 a.m.