peaks_to_bins: Transforms a peaks x cells count matrix into a bins x cells...

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Description

This functions is best used to re-count large number of small peaks (e.g. <= 5000bp) into equal or larger bins. The genome is either cut in fixed bins (e.g. 50,000bp) or into an user defined number of bins. Bins are calculated based on the canconical chromosomes. Note that if peaks are larger than bins, or if peaks are overlapping multiple bins, the signal is added to each bin. Users can increase the minimum overlap to consider peaks overlapping bins (by default 150bp, size of a nucleosome) to disminish the number of peaks overlapping multiple region. Any peak smaller than the minimum overlapp threshold will be dismissed. Therefore, library size might be slightly different from peaks to bins if signal was duplicated into multiple bins or ommitted due to peaks smaller than minimum overlap.

Usage

peaks_to_bins(
  mat,
  bin_width = 50000,
  n_bins = NULL,
  minoverlap = 150,
  verbose = TRUE,
  ref = "hg38"
)

Arguments

mat	A matrix of peaks x cells
bin_width	width of bins to produce in base pairs (minimum 500) (50000)
n_bins	number of bins (exclusive with bin_width)
minoverlap	Minimum overlap between a peak and a bin to consider the peak as overlapping the bin (150).
verbose	Verbose
ref	reference genome to use (hg38)

Value

A sparse matrix of bins instead of peaks

Examples

mat = create_scDataset_raw()$mat
binned_mat = peaks_to_bins(mat,bin_width = 10e6)
dim(binned_mat)

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.