fit.CopyNumberSegmentationModel

CopyNumberSegmentationModel.fit

fit,CopyNumberSegmentationModel-method

A <code><a href="/link/vector?package=aroma.core&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of array indices specifying which arrays to
   be considered.  If <code><a href="/link/NULL?package=aroma.core&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::NULL">NULL</a></code>, all are processed.

arrays

A <code><a href="/link/vector?package=aroma.core&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of chromosomes indices specifying which
    chromosomes to be considered.  If <code><a href="/link/NULL?package=aroma.core&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::NULL">NULL</a></code>, all are processed.

chromosome

A <code><a href="/link/double?package=aroma.core&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::double">double</a></code> in [0,1] indicating how many non-finite
    signals are allowed in the sanity checks of the data.

maxNAFraction

If <code><a href="/link/FALSE?package=aroma.core&version=2.2.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::FALSE">FALSE</a></code>, the model will not be fitted again if it was
    already fitted.

force

Additional arguments passed to the segmentation method for
    the <code><a href="/link/RawGenomicSignals?package=aroma.core&version=2.2.0&to=aroma.core" rd-options="aroma.core" data-mini-rdoc="aroma.core::RawGenomicSignals">RawGenomicSignals</a></code>.

If <code><a href="/link/TRUE?package=aroma.core&version=2.2.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, the segmentation fit structures are
    returned for each fitted array and chromosome.

.retResults

A <code><a href="/link/logical?package=aroma.core&version=2.2.0&to=base" rd-options="base" data-mini-rdoc="base::logical">logical</a></code> or <code><a href="/link/Verbose?package=aroma.core&version=2.2.0&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

methods

internal

This package contains core methods and classes used by
        higher-level aroma.* packages part of the Aroma Project, e.g.
        aroma.affymetrix and aroma.cn.  Its API should be considered to
        be in alpha and beta versions, and is mostly of interest to
        developers.

Henrik Bengtsson

aroma.core

Core methods and classes used by aroma.* package part of The
        Aroma Project

fit.CopyNumberSegmentationModel function

Arguments in <code>...</code> are passed down to the internal fit function,
  which means that it is possible to fine tune even further.

fit.CopyNumberSegmentationModel: Fits the model

Description

Usage

Value

Additional arguments to the internal fit function

See Also