cnv {scPloidy}

Infer Copy Number Variations (CNVs) in Cancer Cells from ATAC-seq Fragment Overlap

Description

Infer Copy Number Variations (CNVs) in Cancer Cells from ATAC-seq Fragment Overlap

Usage

cnv(
  fragmentoverlap,
  windowcovariates,
  levels = c(2, 4),
  nfragspercellmin = 5000,
  nfragspercellmax = 10^5.5,
  deltaBICthreshold = 0
)

Arguments

fragmentoverlap

Frequency of fragment overlap in each cell-window computed by the function fragmentoverlapcount. barcode should be named as AAACGAAAGATTGACA-1.window_1, which represents cell AAACGAAAGATTGACA-1 and window window_1. The format is "cell barcode", ".window_" and integer.

windowcovariates

Chromosomal windows for which copy number gain/loss are initially inferred. Required columns are chr, start, end, window (for example, window_1) and peaks. Peaks is a numeric column representing chromatin accessibility.

levels

Possible values of ploidy. For example, c(2, 4) if the cells can be diploids or tetraploids. The values must be larger than one.

nfragspercellmin

Minimum number of fragments for a cell-window to be eligible.

nfragspercellmax

Maximum number of fragments for a cell-window to be eligible.

deltaBICthreshold

Only the CNVs with deltaBIC smaller than this threshold are adopted.

Value

A list with two elements. CNV is a data frame of the CNVs identified in the dataset. cellwindowCN is a data frame indicating the ploidy for each cell and the inferred standardized copy number for each cell-window.