cnv: Infer Copy Number Variations (CNVs) in Cancer Cells from...

In scPloidy: Infer Ploidy of Single Cells

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.

scPloidy documentation built on May 29, 2024, 10:37 a.m.