copynumber R package with support for extra assembly

This package is a fork of Bioconductor R package ‘copynumber’ with minor modification for supporting extra genome assemblies (e.g. hg38, mm10). The idea from https://github.com/aroneklund/copynumber is adopted to generate ‘hg38’ object, the process is recorded in data-raw/.

This package may be useful for running sequenza with assembly = "hg38" and other software calling copy number segments with ‘copynumber’ package.

Vignette is removed in this package, please read official documentation at https://bioconductor.org/packages/release/bioc/html/copynumber.html.

Hope someday the official package will adopt all necessary genome assemblies.

Update

• 2020-08-20
  • fork code from https://github.com/igordot/copynumber/ to support mm10.
  • add code suggested by @nurmians to bypass bug 1 row arm.data in multipcf().

NOTE

The source code comes from copynumber v1.26.0, any package updates please inform me by issue or email.

Contribution is welcome.

Installation

Install this modified package from GitHub:

# You can install the orignal package from bioconductor fistly
# to install all dependencies
# BiocManager::install("copynumber")

# Then install this hg38-supported package
# remotes::install_github("ShixiangWang/copynumber")
install.packages("copynumber", repos = c('https://shixiangwang.r-universe.dev', 'https://cloud.r-project.org'))

Test copynumber

library(copynumber)

# Test pcf ----------------------------------------------------------------

#Load the lymphoma data set:
data(lymphoma)

#Take out a smaller subset of 3 samples (using subsetData):
sub.lymphoma <- subsetData(lymphoma,sample=1:3)

#First winsorize data to handle outliers:
wins.lymph <- winsorize(sub.lymphoma)

#Run pcf (using small gamma because of low-density data):
pcf.segments <- pcf(data=wins.lymph,gamma=12,Y=sub.lymphoma, assembly = "hg38")


# Test aspcf --------------------------------------------------------------

#Load LogR and BAF data:
data(logR)
data(BAF)

#First winsorize logR to handle outliers:
wins.logR <- winsorize(logR)

#Run aspcf:
aspcf.segments <- aspcf(wins.logR,BAF, assembly = "hg38")

Test sequenza

library(sequenza)
data.file = system.file("extdata", "example.seqz.txt.gz", package="sequenza", mustWork = TRUE)
test = sequenza.extract(data.file, assembly="hg38")