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

Description Usage Arguments Value

View source: R/findCNVs.R

Description

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

Usage

1
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 Nov. 21, 2018, 10:10 a.m.