calculate_gain_or_loss {ChromSCape} | R Documentation

## Estimate the copy gains/loss of tumor vs normal based on log2-ratio of fraction of reads

### Description

Given a SingleCellExperiment object with the slot "logRatio_cytoBand" containing the log2-ratio of the fraction of reads in each cytoband, estimate if the cytoband was lost or acquired a gain in a non-quantitative way. To do so, the quantiles distribution of the normal cells are calculated, and any cytoband below or above will be considered as a loss/gain. The False Discovery Rate is directly proportional to the quantiles.

### Usage

    calculate_gain_or_loss(scExp, controls, quantiles = c(0.05, 0.95))

### Arguments

`scExp` | A SingleCellExperiment with "logRatio_cytoBand" reducedDim slot filled. See `calculate_logRatio_CNA`
`controls` | Sample IDs or Cell IDs of the normal sample to take as reference.
`quantiles` | Quantiles of normal log2-ratio distribution below/above which cytoband is considered to be a loss/gain. (c(0.05,0.95))

### Value

The SCE with the gain or loss in each cytobands in each cells (of dimension cell x cytoband ) in the reducedDim slot "gainOrLoss_cytoBand".

### Examples

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

[Package ChromSCape version 1.2.62 Index]