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.
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:
- chromosome
- start_pos
- end_pos
- band
- 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
)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.
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)).