calculate_cyto_mat {ChromSCape} | R Documentation

## 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")[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")

[Package ChromSCape version 1.2.62 Index]