rawfile_ToBigWig {ChromSCape}R Documentation

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(
  filename,
  BigWig_filename,
  format = "BAM",
  bin_width = 150,
  n_smoothBin = 5,
  ref = "hg38",
  read_size = 101
)

Arguments

filename

Path to the BAM file (with index) or BED file

BigWig_filename

Path to write the output BigWig file

format

File format, either "BAM" or "BED"

bin_width

Bin size for coverage

n_smoothBin

Number of bins for smoothing values

ref

Reference genome.

read_size

Length of the reads.

Value

Writes a BigWig file as output


[Package ChromSCape version 1.3.22 Index]