edpcr: Performs Extended Digital PCR Analysis

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This package is based on a (currently unpublished) algorithm for analysing quantification cycle (Cq) data from digital PCR (dPCR) experiements. This method uses the Conway Maxwell Poisson distribution for the initial distribution of molecules. The package includes functions for extracting, simulating and preparing data for analysis, performing the analysis to find the posterior mode (or maximum likelihood estimate if priors are not used) and/or simulate a posterior sample using MCMC, and plotting data and results.

Author
Philip Wilson
Date of publication
2016-10-19 00:43:20
Maintainer
Philip Wilson <philip.wilson@lgcgroup.com>
License
GPL-3
Version
0.9

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Man pages

conv
Convert between parameterisations
conv.mcmc
Convert MCMC chain between parameterisations
cqmc
Mode and/or MCMC sample of Cq-dPCR posterior
detrend
Detrend Cq data
Exp37a
Digital PCR output file
fetch
Extract Cq data
get.pars0
Get initial Cq-dPCR parameters
llcq
Log-posterior for Cq-dPCR data
mu2lam
Calculate lambda of Conway Maxwell Poisson distribution from...
p2lam
Calculate lambda of Conway Maxwell Poisson distribution from...
p2mu
Calculate mean of Conway Maxwell Poisson distribution from...
plotall
Plot of Cq density/densities and/or density plot of data.
plotden
Density plot of Cq data
plotfun
Plot of Cq distribution
prep
Create cqdat object
rcq
Simulate Cq data

Files in this package

edpcr/DESCRIPTION
edpcr/NAMESPACE
edpcr/R
edpcr/R/conv.R
edpcr/R/conv.mcmc.R
edpcr/R/cqmc.R
edpcr/R/detrend.R
edpcr/R/fetch.R
edpcr/R/get.pars0.R
edpcr/R/llcq.R
edpcr/R/mu2lam.R
edpcr/R/p2lam.R
edpcr/R/p2mu.R
edpcr/R/plotall.R
edpcr/R/plotden.R
edpcr/R/plotfun.R
edpcr/R/prep.R
edpcr/R/rcq.R
edpcr/data
edpcr/data/Exp37a.rdata
edpcr/man
edpcr/man/Exp37a.Rd
edpcr/man/conv.Rd
edpcr/man/conv.mcmc.Rd
edpcr/man/cqmc.Rd
edpcr/man/detrend.Rd
edpcr/man/fetch.Rd
edpcr/man/get.pars0.Rd
edpcr/man/llcq.Rd
edpcr/man/mu2lam.Rd
edpcr/man/p2lam.Rd
edpcr/man/p2mu.Rd
edpcr/man/plotall.Rd
edpcr/man/plotden.Rd
edpcr/man/plotfun.Rd
edpcr/man/prep.Rd
edpcr/man/rcq.Rd