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The "copynumber" R package with support for hg38

This R package is a fork of the "copynumber" package with minimal modifications to support human genome build hg38. The default behavior is unchanged, and it should be safe to use this as a drop-in replacement for the original package.

Note that the default assembly is still hg19 -- so if you want to use hg38 you must specify it explicitly, e.g.

  wins.logR <- winsorize(logR, assembly = "hg38")    
  aspcf.segments <- aspcf(wins.logR,BAF, assembly = "hg38")

Installation

You can install this package directly from GitHub like this:

library("devtools")
install_github("aroneklund/copynumber")

How did I create the hg38 object?

## download cytoband file for hg38
##   http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz

a <- read.delim("cytoBand.txt.gz", header = FALSE)
a2 <- a[a$V1 %in% c('chrX', 'chrY', paste0('chr', 1:22)), ]
a3 <- a2
a3$V1 <- factor(a3$V1)
a3$V4 <- factor(a3$V4)
rownames(a3) <- seq(1:nrow(a3))
hg38 <- a3

## the cytoband data for various genome builds are in this file
oldthings <- load('sysdata.rda')

## we just add hg38 and leave the rest as it was
save(list = c(oldthings, "hg38"), file = 'sysdata.rda')