yunuuuu / copynumber

copynumber with hg38

copynumber with hg38

This is an modified version of the copynumber R package. It has been adjusted to support the human hg38 genome builds (Following the tutorial in https://github.com/aroneklund/copynumber), in addition, it will be okay to provide a customized cytoband data.frame directly.

Assembly usage

Speicifically, this is used for the “assembly” parameter in aspcf, multipcf, pcf, and winsorize functions. We can provide a scalar string or a data.frame directly.

• string Only “hg16”, “hg17”, “hg18”, “hg19”, “hg38”, “mm7”, “mm8” and “mm9” are supported.
• a data.frame with 5 columns (names don’t matter) in the order:
  1. chromosome
  2. start_pos
  3. end_pos
  4. band
  5. gieStain

Notes: it’s easy to do this with:

# assembly should be a genome string like "hg38", "hg19", or "mm9", "mm10".
data.table::fread(
    sprintf("http://hgdownload.cse.ucsc.edu/goldenpath/%s/database/cytoBand.txt.gz",
    assembly),
    header = FALSE
)

Installation

You can install the development version of copynumber from GitHub with:

pak::pkg_install("Yunuuuu/copynumber")

Similar work can also be found in aroneklund, igordot, ShixiangWang. And Irrationone provides a species-agnostic approach.

Official copynumber

Since the official copynumber has been labelled as deprecated and will be removed from Bioconductor version 3.18. This repo also kept a backup of the official copynumber in official branch (You can install it with pak::pkg_install(Yunuuuu/copynumber@official)).