The dpcR package is a collection of functions for a digital Polymerase Chain
Reaction (dPCR) analysis. dPCR comprises methods to quantify nucleic acids,
copy number variations (CNV), homo-/heterozygosity, and rare mutations
(including single nucleotide polymorphisms (SNP)). The chemical basis of
dPCR is similar to conventional PCR but the reaction-mix is divided into
hundredths to thousands of small compartments with parallel amplifications
reactions. The analysis is based on counting the number of positive
compartments and to relate it to the total number of compartments be means
of Poission statistics which enables an absolute quantification.
Arguments
Details
The package includes plot functions, summary functions, data sets and simulations
for dPCR and customizable GUI creators for droplet digital PCRs and
chamber-based digital PCRs. The authors of the package aim to include all
statistical approaches published in peer-review literature and additional
selected sources of expertise currently available and to make them available
to the scientific community in an open and cross-platform environment. As
such the dpcR packages has a list of expressions/functions and may serve in
future a reference to a unified nomenclature in dpcR. The package is
primarily targeted at researchers who which to use it with an existing
technology or during the development of novel digital PCR systems. In
addition the dpcR package provides interactive tools that can be used in
classes or by individuals to better learn about digital PCR concepts and
data interpretation.
References
Huggett J, Foy CA, Benes V, Emslie K, Garson JA, Haynes R,
Hellemans J, Kubista M, Mueller RD, Nolan T, Pfaffl MW, Shipley GL,
Vandesompele J, Wittwer CT, Bustin SA The Digital MIQE Guidelines:
Minimum Information for Publication of Quantitative Digital PCR Experiments
Clinical Chemistry, 2013. 59(6): p.892-902.
Vogelstein B, Kinzler KW, Digital PCR. PNAS, 1999. 96(16): p.
9236-9241.