order_bins: order genome bins based on chromosome and starting position

In SingerLab/gac: Genetic Analysis of Cells

order genome bins based on chromosome and starting position

Description

order genome bins based on chromosome and starting position

Usage

order_bins(
  cnr,
  chromosome.order = c(1:22, "X", "Y", "MT"),
  chrom.column = "bin.chrom",
  start.column = "bin.start"
)

Arguments

cnr	a cnr bundle
chromosome.order	order for chromosomes, default is 1:22, X, Y, and MT, corresponding to the human genome
chrom.column	column name for the bin chromosomes. default "bin.chrom"
start.column	column name for bin start. default "bin.start"

Value

Function returns an chromInfo ordered by bin chromosomes and start coordinates

Examples

data(cnr)

set.seed(2023)
shuffled.bins <- sample(1:nrow(cnr$chromInfo), size = nrow(cnr$chromInfo))
cnr$chromInfo <- cnr$chromInfo[shuffled.bins, ]
head(cnr$chromInfo)

cnrS <- order_bins(cnr)
head(cnrS$chromInfo)

SingerLab/gac documentation built on March 23, 2024, 5:15 a.m.