DNAcopy.findCNVs: Find copy number variations (DNAcopy, univariate)

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Find copy number variations (DNAcopy, univariate)

Description

DNAcopy.findCNVs classifies the binned read counts into several states which represent copy-number-variation.

Usage

DNAcopy.findCNVs(binned.data, ID = NULL, CNgrid.start = 1.5, strand = "*")

Arguments

binned.data	A GRanges-class object with binned read counts.
ID	An identifier that will be used to identify this sample in various downstream functions. Could be the file name of the binned.data for example.
CNgrid.start	Start parameter for the CNgrid variable. Very empiric. Set to 1.5 for normal data and 0.5 for Strand-seq data.
strand	Find copy-numbers only for the specified strand. One of c('+', '-', '*').

Value

An aneuHMM object.

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.