plot-methods

plot,CNVDetectionResult,missing-method

The index of the CNV region to be plotted.

which

Vector of two positive integers that states
  how many segments left and right of the CNV region should
  be included in the plot. Default = c(10,10).

margin

Logical value whether the output should be
  plotted to a file. Default = FALSE.

toFile


  Plots read counts, call values and CNV calls in an
  identified CNV region.


plot

cn.mops (Copy Number estimation by a Mixture Of PoissonS)
is a data processing pipeline for copy number variations and
aberrations (CNVs and CNAs) from next generation sequencing
(NGS) data. The package supplies functions to convert BAM files
into read count matrices or genomic ranges objects, which are
the input objects for cn.mops. cn.mops models the depths of
coverage across samples at each genomic position. Therefore, it
does not suffer from read count biases along chromosomes. Using
a Bayesian approach, cn.mops decomposes read variations across
samples into integer copy numbers and noise by its mixture
components and Poisson distributions, respectively. cn.mops
guarantees a low FDR because wrong detections are indicated by
high noise and filtered out. cn.mops is very fast and written
in C++.

plot: Plots a CNVDetectionResult

Description

Usage

Arguments

Value