get_cyto_features {ChromSCape}R Documentation

Map features onto cytobands

Description

Map the features of a SingleCellExperiment onto the cytobands of a given genome. Some features might not be mapped to any cytobands (e.g. if they are not in the canconical chromosomes), and are removed from the returned object.

Usage

get_cyto_features(scExp, ref_genome = c("hg38", "mm10")[1])

Arguments

scExp

A SingleCellExperiment with genomic coordinate as features (peaks or bins)

ref_genome

Reference genome ('hg38' or 'mm10')

Details

The cytobands are an arbitrary cutting of the genome that dates back to staining metaphase chromosomes with Giemsa.

Value

A data.frame of the SCE features with their corresponding cytoband name

Examples

data("scExp")
matching_cyto = get_cyto_features(scExp, ref_genome="hg38")
 

[Package ChromSCape version 1.4.0 Index]