edivisive.findCNVs {AneuFinder} | R Documentation

## Find copy number variations (edivisive, univariate)

### Description

Classify the binned read counts into several states which represent copy-number-variation. The function uses the `e.divisive` function to segment the genome.

### Usage

    edivisive.findCNVs(binned.data, ID = NULL, CNgrid.start = 1.5,
      strand = "*", R = 10, sig.lvl = 0.1)

### 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('+', '-', '*')`.
`R` | method-edivisive: The maximum number of random permutations to use in each iteration of the permutation test (see `e.divisive`). Increase this value to increase accuracy on the cost of speed.
`sig.lvl` | method-edivisive: The level at which to sequentially test if a proposed change point is statistically significant (see `e.divisive`). Increase this value to find more breakpoints.

### Value

An `aneuHMM` object.

[Package AneuFinder version 1.12.1 Index]