calculate_logRatio_CNA {ChromSCape} | R Documentation

## Calculate the log2-ratio of tumor vs normal fraction of reads in cytobands

### Description

Given a SingleCellExperiment object with the slot "cytoBand" containing the fraction of reads in each cytoband, calculates the log2-ratio of tumor vs normal fraction of reads in cytobands, cell by cell. If the average signal in normal sample in a cytoband is 0, set this value to 1 so that the ratio won't affect the fraction of read value.

### Usage

    calculate_logRatio_CNA(scExp, controls)

### Arguments

`scExp` | A SingleCellExperiment with "cytoBand" reducedDim slot filled. see `calculate_cyto_mat`
`controls` | Sample IDs or Cell IDs of the normal sample to take as reference.

### Value

The SCE with the log2-ratio of fraction of reads in each cytobands in each cells (of dimension cell x cytoband ) in the reducedDim slot "logRatio_cytoBand".

### Examples

    data("scExp")
    scExp = calculate_cyto_mat(scExp, ref_genome="hg38")
    scExp = calculate_logRatio_CNA(scExp, controls=unique(scExp$sample_id)[1])
    SingleCellExperiment::reducedDim(scExp, "logRatio_cytoBand")

[Package ChromSCape version 1.2.62 Index]