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- and heterozygosity, as well as 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 relating it to the total number of compartments by 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 for droplet digital PCRs and
array-based digital PCRs. We aim to include all
statistical approaches published in peer-review literature and additional
selected sources of expertise currently available. We intent to make these methods
available to the scientific community in an open and cross-platform environment. Using
the naming convention derived from the MIQE Guidelines for digital PCR, we hope to
become a reference to a unified nomenclature in dpcR.
The package is primarily targeted at researchers who wish 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 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.