ShotgunFunctionalizeR - an R-package for functional comparison of metagenomes

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Documentation for package ‘ShotgunFunctionalizeR’ version 1.2-9

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ShotgunFunctionalizeR-package ShotgunFunctionalizeR - an R-package for shotgun metagenomic analysis
calculatePoissonR2 Calculates the goodness-of-fit for Poisson regression
calculateRarefaction Calculates rarefaction curves
clusterSamples Performs hierarchical clustering on a set of samples
countCategories Counts the occurrences of gene categories
densityPlot Plotting the distribution of counts for a metagenome
diversityPlot.family Calculates and plots rarefaction curves
estimateDiversity Estimate diversity indices for a data set
freqPlot.family Plots the relative abundance of a gene family
getSamples Select a subset of samples
getSupportedFamilies Returns the supported gene families
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
OceanPFAM Metagenomes sampled at multiple depth in the Pacific Ocean annotated as PFAM domains
OceanTIGR Metagenomes sampled at multiple depth in the Pacific Ocean annotated as TIGRfam domains
ppPlot Observed and theoretical p-value quantiles
readGeneFamilies Read a data file
ShotgunFunctionalizeR ShotgunFunctionalizeR - an R-package for shotgun metagenomic analysis
ShotgunFunctionalizeRAnnotationData System data for ShotgunFunctionalizeR
summarizeData Statistical summary for a set of metagenomes
testGeneCategories Performs a pathway-centric test for identification of significant gene family categories
testGeneCategories.dircomp Performs a pathway-centric analysis using Poisson direct comparison
testGeneCategories.enrichment Performs a pathway-centric test using a test of overrepresentation
testGeneCategories.gaussiansum Performs a pathway-centric analysis using Gaussian Sum statistics
testGeneCategories.independence Performs a pathway-centric test using a test of independence
testGeneCategories.poisson Performs a pathway-centric test using a Poisson model
testGeneCategories.regression Performs a pathway-centric analysis using Poisson regression analysis
testGeneFamilies Performs a gene-centric test for identification of significant gene families
testGeneFamilies.binomial Performs a gene-centric analysis using a binomial test
testGeneFamilies.dircomp Performs a gene-centric analysis using Poisson direct comparison
testGeneFamilies.gaussian Performs a gene-centric analysis using a Gaussian test
testGeneFamilies.hypergeometric Performs a gene-centric analysis using a hypergeometric test
testGeneFamilies.poisson Performs a gene-centric test using a Poisson model
testGeneFamilies.regression Performs a gene-centric analysis using Poisson 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