calculate_CNA {ChromSCape} | R Documentation

## Estimate copy number alterations in cytobands

### Description

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. The function successively :

- Calculates the fraction of reads in each cytoband (FrCyto). See `calculate_cyto_mat`

- Calculates the log2-ratio FrCyto of each cell by the average FrCyto in normal cells. See `calculate_logRatio_CNA`

- Estimates if there was a gain or a loss of copy in each cyto band. See `calculate_gain_or_loss`

The corresponding matrices are accessibles in the reducedDim slots "cytoBands", "logRatio_cytoBands" and "gainOrLoss_cytoBands" respectively.

### Usage

    calculate_CNA(
      scExp,
      control_samples = unique(scExp$sample_id)[1],
      ref_genome = c("hg38", "mm10")[1],
      quantiles_to_define_gol = c(0.05, 0.95)
    )

### Arguments

`scExp` | A SingleCellExperiment with "logRatio_cytoBand" reducedDim slot filled. See `calculate_logRatio_CNA`
`control_samples` | Sample IDs of the normal sample to take as reference.
`ref_genome` | Reference genome ('hg38' or 'mm10')
`quantiles_to_define_gol` | Quantiles of normal log2-ratio distribution below/above which cytoband is considered to be a loss/gain. (c(0.05,0.95)). See `calculate_gain_or_loss`

### Value

The SCE with the fraction of reads, log2-ratio and gain or loss in each cytobands in each cells (of dimension cell x cytoband) in the reducedDim slots.

### Examples

    data("scExp")
    scExp = calculate_CNA(scExp,  control_samples = unique(scExp$sample_id)[1],
    ref_genome="hg38", quantiles_to_define_gol = c(0.05,0.95))
    SingleCellExperiment::reducedDim(scExp, "cytoBand")
    SingleCellExperiment::reducedDim(scExp, "logRatio_cytoBand")
    SingleCellExperiment::reducedDim(scExp, "gainOrLoss_cytoBand")

[Package ChromSCape version 1.2.62 Index]