calculate_cyto_mat: Calculate Fraction of reads in each cytobands

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

Calculate Fraction of reads in each cytobands

Description

Re-Count binned reads onto cytobands and calculate the fraction of reads in each of the cytoband in each cell. For each cell, the fraction of reads in any given cytoband is calculated. Cytobands are considered large enough in order that a variation at the cytoband level is not considered as an epigenetic event but as a genetic event, e.g. Copy Number Alterations.

Usage

calculate_cyto_mat(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')

Value

The SCE with the fraction of reads in each cytobands in each cells (of dimension cell x cytoband ) in the reducedDim slot "cytoBand".

Examples

data("scExp")
scExp = calculate_cyto_mat(scExp, ref_genome="hg38")
SingleCellExperiment::reducedDim(scExp, "cytoBand") 

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