rawfile_ToBigWig: rawfile_ToBigWig : reads in BAM file and write out BigWig...

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

rawfile_ToBigWig : reads in BAM file and write out BigWig coverage file, normalized and smoothed

Description

rawfile_ToBigWig : reads in BAM file and write out BigWig coverage file, normalized and smoothed

Usage

rawfile_ToBigWig(
  input,
  BigWig_filename,
  format = "BAM",
  bin_width = 150,
  norm_factor,
  n_smoothBin = 5,
  ref = "hg38",
  read_size = 101,
  original_bins = NULL,
  quantile_for_peak_calling = 0.85
)

Arguments

input	Either a named list of character vector of path towards single-cell BED files or a sparse raw matrix of small bins (<<500bp). If a named list specifying scBEDn the names MUST correspond to the 'sample_id' column in your SingleCellExperiment object. The single-cell BED files names MUST match the barcode names in your SingleCellExperiment (column 'barcode'). The scBED files can be gzipped or not.
BigWig_filename	Path to write the output BigWig file
format	File format, either "BAM" or "BED"
bin_width	Bin size for coverage
norm_factor	Then number of cells or total number of reads in the given sample, for normalization.
n_smoothBin	Number of bins for smoothing values
ref	Reference genome.
read_size	Length of the reads.
original_bins	Original bins GenomicRanges in case the format is raw matrix.
quantile_for_peak_calling	The quantile to define the threshold above which signal is considered as a peak.

Value

Writes in the output directory a bigwig file displaying the cumulative coverage of cells and a basic set of peaks called by taking all peaks above a given threshold

Writes a BigWig file as output

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.