MCMC.qpcr: Bayesian Analysis of qRT-PCR Data

Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: <http://bit.ly/1Nwo4CB>.

Author
Mikhail V. Matz
Date of publication
2016-11-09 23:56:55
Maintainer
Mikhail V. Matz <matz@utexas.edu>
License
GPL-3
Version
1.2.3

View on CRAN

Man pages

amp.eff
amplification efficiencies and experimental Cq1 (optional...
beckham.data
Cellular heat stress response data.
beckham.eff
amplification efficiencies for beckham.data
coral.stress
RT-qPCR of stress response in coral Porites astreoides
cq2counts
Prepares qRT-PCR data for mcmc.qpcr analysis
cq2genorm
Reformats raw Ct data for geNorm analysis (non-parametric...
cq2log
Prepares qRT-PCR data for mcmc.qpcr analysis using lognormal...
diagnostic.mcmc
Plots three diagnostic plots to check the validity of the...
dilutions
Data to determine amplification efficiency
getNormalizedData
Extracts qPCR model predictions
HPDplot
Plotting fixed effects for all genes for a single combination...
HPDplotBygene
Plots qPCR analysis results for individual genes.
HPDplotBygeneBygroup
Plots qPCR analysis results for individual genes
HPDpoints
HPDplot, HPDpoints
HPDsummary
Summarizes and plots results of mcmc.qpcr function series.
mcmc.converge.check
MCMC diagnostic plots
mcmc.pval
calculates p-value based on Bayesian z-score or MCMC sampling
mcmc.qpcr
Analyzes qRT-PCR data using generalized linear mixed model
mcmc.qpcr.classic
Analyzes qRT-PCR data using "classic" model, based on...
mcmc.qpcr.lognormal
Fits a lognormal linear mixed model to qRT-PCR data.
MCMC.qpcr-package
Bayesian analysis of qRT-PCR data
normalize.qpcr
Internal function called by mcmc.qpcr.classic
outlierSamples
detects outlier samples in qPCR data
padj.qpcr
Calculates adjusted p-values corrected for multiple...
PrimEff
Determines qPCR amplification efficiencies from dilution...
softNorm
Accessory function to mcmc.qpcr() to perform soft...
summaryPlot
Wrapper function for ggplot2 to make bar and line graphs of...
trellisByGene
For two-way designs, plots mcmc.qpcr model predictions gene...

Files in this package

MCMC.qpcr
MCMC.qpcr/NAMESPACE
MCMC.qpcr/data
MCMC.qpcr/data/dilutions.rda
MCMC.qpcr/data/beckham.eff.rda
MCMC.qpcr/data/amp.eff.rda
MCMC.qpcr/data/coral.stress.rda
MCMC.qpcr/data/beckham.data.rda
MCMC.qpcr/R
MCMC.qpcr/R/cq2counts.R
MCMC.qpcr/R/mcmc.qpcr.classic.R
MCMC.qpcr/R/cq2log.R
MCMC.qpcr/R/mcmc.qpcr.R
MCMC.qpcr/R/summaryPlot.R
MCMC.qpcr/R/HPDplotBygeneBygroup.R
MCMC.qpcr/R/HPDpoints.R
MCMC.qpcr/R/HPDplotBygene.R
MCMC.qpcr/R/mcmc.qpcr.lognormal.R
MCMC.qpcr/R/diagnostic.mcmc.R
MCMC.qpcr/R/softNorm.R
MCMC.qpcr/R/cq2genorm.R
MCMC.qpcr/R/mcmc.converge.check.R
MCMC.qpcr/R/PrimEff.R
MCMC.qpcr/R/normalize.qpcr.R
MCMC.qpcr/R/mcmc.pval.R
MCMC.qpcr/R/padj.qpcr.R
MCMC.qpcr/R/HPDplot.R
MCMC.qpcr/R/outlierSamples.R
MCMC.qpcr/R/getNormalizedData.R
MCMC.qpcr/R/trellisByGene.R
MCMC.qpcr/R/HPDsummary.R
MCMC.qpcr/MD5
MCMC.qpcr/DESCRIPTION
MCMC.qpcr/man
MCMC.qpcr/man/trellisByGene.Rd
MCMC.qpcr/man/mcmc.converge.check.Rd
MCMC.qpcr/man/mcmc.qpcr.Rd
MCMC.qpcr/man/cq2counts.Rd
MCMC.qpcr/man/mcmc.pval.Rd
MCMC.qpcr/man/outlierSamples.Rd
MCMC.qpcr/man/MCMC.qpcr-package.Rd
MCMC.qpcr/man/getNormalizedData.Rd
MCMC.qpcr/man/summaryPlot.Rd
MCMC.qpcr/man/softNorm.Rd
MCMC.qpcr/man/HPDsummary.Rd
MCMC.qpcr/man/normalize.qpcr.Rd
MCMC.qpcr/man/coral.stress.Rd
MCMC.qpcr/man/beckham.eff.Rd
MCMC.qpcr/man/cq2log.Rd
MCMC.qpcr/man/mcmc.qpcr.lognormal.Rd
MCMC.qpcr/man/HPDplotBygene.Rd
MCMC.qpcr/man/cq2genorm.Rd
MCMC.qpcr/man/beckham.data.Rd
MCMC.qpcr/man/HPDpoints.Rd
MCMC.qpcr/man/dilutions.Rd
MCMC.qpcr/man/HPDplot.Rd
MCMC.qpcr/man/HPDplotBygeneBygroup.Rd
MCMC.qpcr/man/padj.qpcr.Rd
MCMC.qpcr/man/amp.eff.Rd
MCMC.qpcr/man/PrimEff.Rd
MCMC.qpcr/man/mcmc.qpcr.classic.Rd
MCMC.qpcr/man/diagnostic.mcmc.Rd