snpsNByTotalAndFracB.matrix

snpsNByTotalAndFracB

An Jx2xI <code><a rd-options="base" href="/link/numeric?package=NSA&version=0.0.32&to=base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a rd-options="base" href="/link/array?package=NSA&version=0.0.32&to=base" data-mini-rdoc="base::array">array</a></code>, where J is the number of loci,
                      2 is total and fracB, and I is the number of samples.

data

A <code><a rd-options="base" href="/link/logical?package=NSA&version=0.0.32&to=base" data-mini-rdoc="base::logical">logical</a></code> or <code><a rd-options="base" href="/link/numeric?package=NSA&version=0.0.32&to=base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a rd-options="base" href="/link/vector?package=NSA&version=0.0.32&to=base" data-mini-rdoc="base::vector">vector</a></code> specifying which
     samples should be used as the reference set.
     By default, all samples are considered.

references

See <code><a rd-options="R.utils" href="/link/Verbose?package=NSA&version=0.0.32&to=R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose


  Normalize allele-specific copy numbers (total,fracB), where total is the total (non-polymorphic) signal and
  fracB is the allele B fraction.
  It is only loci with a non-missing (<code><a rd-options="base" href="/link/NA?package=NSA&version=0.0.32&to=base" data-mini-rdoc="base::NA">NA</a></code>) fracB value that are
  considered to be SNPs and normalized by CalMaTe.  The other loci
  are left untouched.
 

snpsNByTotalAndFracB.matrix: Normalize allele-specific copy numbers (total,fracB)

Description

Usage

Arguments

Value