order_genes: order gene.index based on chromosome and starting coordinate

In SingerLab/gac: Genetic Analysis of Cells

order gene.index based on chromosome and starting coordinate

Description

order gene.index based on chromosome and starting coordinate

Usage

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

Value

Function returns an gene.index ordered by chromosomes and start

Examples

data(cnr)

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

cnrS <- order_genes(cnr)

head(cnrS$gene.index)

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