get_cyto_features: Map features onto cytobands

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

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", "ce11")[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")
 

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.