get_most_variable_cyto: Retrieve the cytobands with the most variable fraction of...

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

Retrieve the cytobands with the most variable fraction of reads

Description

Given a SingleCellExperiment object with the slot "cytoBand" containing the fraction of reads in each cytoband, calculates the variance of each cytoband and returns a data.frame with the top variables cytobands. Most cytobands are expected to be unchanged between normal and tumor samples, therefore focusing on the top variable cytobands enable to focus on the most interseting regions.

Usage

get_most_variable_cyto(scExp, top = 50)

Arguments

scExp	A SingleCellExperiment with "cytoBand" reducedDim slot filled.
top	Number of cytobands to return (50).

Value

A data.frame of the top variable cytoBands and their variance

Examples

data("scExp")
scExp = calculate_cyto_mat(scExp, ref_genome="hg38")
get_most_variable_cyto(scExp, top=50)
 

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