Associate peaks to genes based on distance to TSS (or gene body)

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

vector(character) - List of peaks.

genes

vector(character) - List of genes.

sep

vector(character) - Separator between chromosome, start and end position. Default: c('-', '-').

method

(character) - Method to use. Default: "Signac".

'Signac' - Use Signac::Extend to extend genes.
'GREAT' - Not implemented yet.

upstream

(int) - Upstream distance from TSS to consider as potential promoter.

downstream

(int) - Downstream distance from TSS to consider as potential promoter.

extend

(int) - Integer defining the distance from the upstream and downstream of the basal regulatory region. Used only by method 'GREAT'.

only_tss

(logical) - If TRUE, only TSS will be considered.

verbose

(logical) - If TRUE, print progress messages.

Value

(matrix) - Matrix of peaks x genes with 1 if peak is near gene.

Examples

TODO
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