ShotgunFunctionalizeR - an R-package for functional comparison of metagenomes


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Documentation for package ‘ShotgunFunctionalizeR’ version 1.0-3

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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