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 |