calculate_gain_or_loss: Estimate the copy gains/loss of tumor vs normal based on...

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

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")

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