subsetCNR: Subset a set of bins or genes from a CNR object

In SingerLab/gac: Genetic Analysis of Cells

Subset a set of bins or genes from a CNR object

Description

This function pulls out a section of the genome for further analysis.

Usage

subsetCNR(
  cnr,
  bins = NULL,
  genes = NULL,
  chrom = NULL,
  start = NULL,
  end = NULL,
  ...
)

Arguments

cnr	a cnr bundle
bins	a vector of bins to keep
genes	a vector of genes to keep
chrom	a vector of chromosomes, or single chromosome if genomic coordinates are used
start	a start position
end	an end position
...	additional parameters e.g. padding to add bins when coordinates are used

Value

Returns a cnr object with only the desired bins. This function also subsets the gene index and chromInfo as well

Examples

data(cnr)
data(segCol)

## subset based on bins
bins1.100 <- subsetCNR(cnr, bins = 1:100)

## subset based on genes
genes.3 <- subsetCNR(cnr, genes = c("CDK4", "MDM2", "HMGA2", "TP53"))

## subset based on chromosomes
chrom6.12 <- subsetCNR(cnr, chrom = c(6, 12))

## subset based on genomic coordinates
chrom12q13.15 <- subsetCNR(cnr, chrom = 12, start = 46000000, end = 71000000)

SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.