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| ShotgunFunctionalizeR-package | ShotgunFunctionalizeR - an R-package for shotgun metagenomic analysis ~~ package title ~~ |
| calculatePoissonR2 | Calculates the goodness-of-fit for Poisson regression |
| densityPlot | Plotting the distribution of counts for a metagenome |
| getAnnotation | Annotates a list of gene family accession numbers |
| groupPlot | Plots the result from a direct comparison using the Poisson model |
| groupPlot.category | Plots the result from a pathway-centric direct comparison using the Poisson model |
| groupPlot.family | Plots the result from a gene-centric direct comparison using the Poisson model |
| MouseCOG | Metagenomic data from mouse gut annotated as COGs |
| MouseEC | Metagenomic data from mouse gut annotated as EC numbers |
| OceanCOG | Metagenomes sampled at multiple depth in the Pacific Ocean annotated as COGs |
| OceanEC | Metagenomes sampled at multiple depth in the Pacific Ocean annotated as EC numbers |
| ppPlot | Observed and theoretical p-value quantiles |
| readGeneFamilies | Read a data file |
| ShotgunFunctionalizeR | ShotgunFunctionalizeR - an R-package for shotgun metagenomic analysis ~~ package title ~~ |
| ShotgunFunctionalizeRAnnotationData | System data for ShotgunFunctionalizeR |
| summarizeData | Statistical summary for a set of metagenomes |
| testGeneCategories | Tests for significant gene categories |
| testGeneCategories.dircomp | Tests for significant gene families using direct comparison |
| testGeneCategories.enrichment | Tests for significant gene categories using enrichment |
| testGeneCategories.gaussiansum | Tests for significant gene categories using the Gaussian sum statistic |
| testGeneCategories.independence | Tests for significant gene categories using the Gaussian sum statistic |
| testGeneCategories.poisson | Tests for significant gene categories using the Gaussian sum statistic |
| testGeneCategories.regression | Tests for significant gene families using regression analysis |
| testGeneFamilies | Tests for significant gene families |
| testGeneFamilies.binomial | Identified significant gene families between two samples using the binomial model |
| testGeneFamilies.dircomp | Tests for significant gene families using direct comparison |
| testGeneFamilies.gaussian | Identified significant gene families between two samples using the gaussian model |
| testGeneFamilies.hypergeometric | Identified significant gene families between two samples using the hypergeometric model |
| testGeneFamilies.poisson | Identified significant gene families using the poisson model |
| testGeneFamilies.regression | Tests for significant gene families using regression analysis |
| trendPlot | Plots the result from a regression analysis using the Poisson model |
| trendPlot.category | Plots the result from a gene-centric direct comparison using the Poisson model |
| trendPlot.family | Plots the result from a gene-centric direct comparison using the Poisson model |
| writeRankings | Writes rankings to a file |