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

Description Usage Arguments Value

View source: R/findCNVs.R

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

1
2
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.


ataudt/aneufinder documentation built on Nov. 21, 2018, 10:10 a.m.