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.

genes

A GRanges object with gene coordinates.

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.

method

Character specifying the method to link peak overlapping motif regions to nearby genes. On of 'Signac' or 'GREAT'.

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 value. Measure distance from the TSS (TRUE) or from the entire gene body (FALSE).

verbose

Logical value. Display messages

Value

A sparse binary Matrix with gene/peak matches.