Find peaks or regions near gene body or TSS

Find peaks or regions near gene body or TSS

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.