R: Bayesian Analysis of qRT-PCR Data

# Bayesian Analysis of qRT-PCR Data

## Documentation for package ‘MCMC.qpcr’ version 1.2.4

- DESCRIPTION file

## Help Pages

amp.eff | amplification efficiencies and experimental Cq1 (optional column)
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 selection of stable control genes) as implemented in selectHKgenes function (package SLqPCR)
cq2log | Prepares qRT-PCR data for mcmc.qpcr analysis using lognormal and "classic" (normalization-based) models
diagnostic.mcmc | Plots three diagnostic plots to check the validity of the assumptions of linear model analysis.
dilutions | Data to determine amplification efficiency
getNormalizedData | Extracts qPCR model predictions
HPDplot | Plotting fixed effects for all genes for a single combination of factors
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 | Bayesian analysis of qRT-PCR data
mcmc.qpcr | Analyzes qRT-PCR data using generalized linear mixed model
mcmc.qpcr.classic | Analyzes qRT-PCR data using "classic" model, based on multigene normalization.
mcmc.qpcr.lognormal | Fits a lognormal linear mixed model to qRT-PCR data.
normalize.qpcr | Internal function called by mcmc.qpcr.classic
outlierSamples | detects outlier samples in qPCR data
padj.hpdsummary | Adjusts p-values within an HPDsummary() object for multiple comparisons
padj.qpcr | Calculates adjusted p-values corrected for multiple comparisons
PrimEff | Determines qPCR amplification efficiencies from dilution series
softNorm | Accessory function to mcmc.qpcr() to perform soft normalization
summaryPlot | Wrapper function for ggplot2 to make bar and line graphs of mcmc.qpcr() results
trellisByGene | For two-way designs, plots mcmc.qpcr model predictions gene by gene