multi.bigwig.mean: Multi-bigWig average tool

In sebastian-gregoricchio/Rseb: An R-package for NGS data managing and visualization

Multi-bigWig average tool

Description

This tools uses bigwigCompare (see details) to perform the average between multiple bigWig files in a multi-step process.

Usage

multi.bigwig.mean(
  sample.config,
  output.dir = file.path(getwd(), "merged_bigWigs"),
  bin.size = 50,
  merged.suffix = paste0("_merged_bs", format(ceiling(bin.size), scientific = FALSE)),
  out.file.format = "bigwig",
  number.of.processors = 4,
  bigwigCompare = "bigwigCompare",
  return.log = FALSE,
  verbose = TRUE
)

Arguments

sample.config	A data.frame or a string indicating the path to a table. The table/data.frame must contain in the first column the file list, while the second column the group to which belong each file. Files belonging to the same group will be merged together. The group name corresponds to the name of the corresponding output file.
output.dir	String of the path to the output directory. Default: file.path(getwd(), "merged_bigWigs").
bin.size	Size of the bins in base-pairs (bp). Default: 50.
merged.suffix	Suffix to use for the resulting output files: <group.id><suffix><extension>. Default: paste0("_merged_bs", format(ceiling(bin.size), scientific = FALSE)).
out.file.format	Output file format. Possible choices: "bigWig", "bw", "bedGraph", "bdg". Default: "bigwig".
number.of.processors	Number of CPUs to use. Default: 4.
bigwigCompare	String of the path to the bigwigCompare tool. Default: "~/.conda/envs/snakepipes/b9364eb954bd13fe4e5f104fa8a286e6/bin/bigwigCompare".
return.log	Logic value to define whether the log list of the bigwigCompare steps performed by 'group.id'. Default: TRUE.
verbose	Logic value to define whether the function should print messages. Default: TRUE.

Details

For details on bigwigCompare visit: https://deeptools.readthedocs.io/en/develop/content/tools/bigwigCompare.html

Value

A list of vectors with the commands used to run bigwigCompare at each step. Each element is one group ID.

sebastian-gregoricchio/Rseb documentation built on May 15, 2024, 5:45 a.m.