fitNaiveGenotypes

fitNaiveGenotypes.numeric

A <code><a rd-options="base" href="/link/numeric?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a rd-options="base" href="/link/vector?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of length J containing allele B fractions
   for a normal sample.

An optional <code><a rd-options="base" href="/link/numeric?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a rd-options="base" href="/link/vector?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of length J specifying the true
   total copy number in $\{0,1,2,NA\}$ at each locus.  This can be
   used to specify which loci are diploid and which are not, e.g.
   autosomal and sex chromosome copy numbers.

An optional <code><a rd-options="base" href="/link/integer?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::integer">integer</a></code> or <code><a rd-options="base" href="/link/logical?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::logical">logical</a></code> <code><a rd-options="base" href="/link/vector?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::vector">vector</a></code> specifying
   which loci should be used for estimating the model.
   If <code><a rd-options="base" href="/link/NULL?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::NULL">NULL</a></code>, all loci are used.

subsetToFit

A <code><a rd-options="base" href="/link/character?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::character">character</a></code> string specifying the type of algorithm used.

flavor

A postive <code><a rd-options="base" href="/link/double?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::double">double</a></code> specifying the amount smoothing for
   the empirical density estimator.

adjust

Additional arguments passed to <code><a rd-options="" href="/link/findPeaksAndValleys?package=aroma.light&version=3.2.0" data-mini-rdoc="aroma.light::findPeaksAndValleys">findPeaksAndValleys</a></code>().

A <code><a rd-options="base" href="/link/double?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::double">double</a></code> <code><a rd-options="base" href="/link/vector?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of length two specifying the range
   for which values are considered finite.  Values below (above) this
   range are treated as -<code><a rd-options="base:is.finite" href="/link/Inf?package=aroma.light&version=3.2.0&to=base%3Ais.finite" data-mini-rdoc="base:is.finite::Inf">Inf</a></code> (+<code><a rd-options="base:is.finite" href="/link/Inf?package=aroma.light&version=3.2.0&to=base%3Ais.finite" data-mini-rdoc="base:is.finite::Inf">Inf</a></code>).

censorAt

A <code><a rd-options="base" href="/link/logical?package=aroma.light&version=3.2.0&to=base" data-mini-rdoc="base::logical">logical</a></code> or a <code><a rd-options="R.utils" href="/link/Verbose?package=aroma.light&version=3.2.0&to=R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code> object.

verbose


  Fit naive genotype model from a normal sample.


methods

Methods for microarray analysis that take basic data types such as matrices and lists of vectors.  These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

Henrik Bengtsson

aroma.light

Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

fitNaiveGenotypes function

A <code><a href="numeric" rd-options="base">numeric</a></code> <code><a href="vector" rd-options="base">vector</a></code> of length J containing allele B fractions
   for a normal sample.

An optional <code><a href="numeric" rd-options="base">numeric</a></code> <code><a href="vector" rd-options="base">vector</a></code> of length J specifying the true
   total copy number in ${0,1,2,NA}$ at each locus.  This can be
   used to specify which loci are diploid and which are not, e.g.
   autosomal and sex chromosome copy numbers.

An optional <code><a href="integer" rd-options="base">integer</a></code> or <code><a href="logical" rd-options="base">logical</a></code> <code><a href="vector" rd-options="base">vector</a></code> specifying
   which loci should be used for estimating the model.
   If <code><a href="NULL" rd-options="base">NULL</a></code>, all loci are used.

A <code><a href="character" rd-options="base">character</a></code> string specifying the type of algorithm used.

A postive <code><a href="double" rd-options="base">double</a></code> specifying the amount smoothing for
   the empirical density estimator.

Additional arguments passed to <code><a href="findPeaksAndValleys" rd-options="">findPeaksAndValleys</a></code>().

A <code><a href="double" rd-options="base">double</a></code> <code><a href="vector" rd-options="base">vector</a></code> of length two specifying the range
   for which values are considered finite.  Values below (above) this
   range are treated as -<code><a href="Inf" rd-options="base:is.finite">Inf</a></code> (+<code><a href="Inf" rd-options="base:is.finite">Inf</a></code>).

A <code><a href="logical" rd-options="base">logical</a></code> or a <code><a href="Verbose" rd-options="R.utils">Verbose</a></code> object.

Fit naive genotype model from a normal sample.

fitNaiveGenotypes: Fit naive genotype model from a normal sample

Description

Usage

Arguments

Value

See Also