calculate_cyto_mat {ChromSCape} | R Documentation |
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.
calculate_cyto_mat(scExp, ref_genome = c("hg38", "mm10")[1])
scExp |
A SingleCellExperiment with genomic coordinate as features (peaks or bins) |
ref_genome |
Reference genome ('hg38' or 'mm10') |
The SCE with the fraction of reads in each cytobands in each cells (of dimension cell x cytoband ) in the reducedDim slot "cytoBand".
data("scExp") scExp = calculate_cyto_mat(scExp, ref_genome="hg38") SingleCellExperiment::reducedDim(scExp, "cytoBand")