Man pages for Russel88/DAtest
Comparing Differential Abundance methods

add.tax.DAAdd tax_table from phyloseq object
allDARun many differential abundance/expression methods
DA.adxAldex t.test and wilcox
DA.ancANCOM
DA.anovaRun 'anova' on all features from 'DAtest' results with...
DA.aovANOVA
DA.baybaySeq
DA.drop1Run 'drop1' on all features from 'DAtest' results with...
DA.ds2DESeq2 with manual geometric means
DA.ds2xDESeq2
DA.ereEdgeR exact test - TMM normalization
DA.ere2EdgeR exact test - RLE normalization
DA.erqEdgeR quasi-likelihood - TMM normalization
DA.erq2EdgeR quasi-likelihood - RLE normalization
DA.friFriedman Rank Sum test
DA.kruKruskal-Wallis test
DA.laoANOVA
DA.lao2ANOVA
DA.limLIMMA
DA.lliLIMMA
DA.lli2LIMMA
DA.llmLog linear regression
DA.llm2Log linear regression
DA.lrmLinear regression
DA.lsmeansRun 'lsmeans' on all features from 'DAtest' results with...
DA.lttWelch t-test
DA.ltt2Welch t-test
DA.msfMetagenomeSeq Feature model
DA.mvaMvabund
DA.nebNegative binomial glm
DA.peaPearson Correlation
DA.perPermutation test of user-defined test statistic
DA.phyloseqExtract data from a 'phyloseq' object to be used in 'DAtest'
DA.poiPoisson glm
DA.qpoQuasi-poisson glm
DA.quaQuade test
DA.raiRAIDA
DA.samSAMSeq
DA.speSpearman's Rank Correlation
DA.tttWelch t-test
DA.TukeyHSDRun 'TukeyHSD' on all features from 'DAtest' results with...
DA.vliLIMMA with 'voom'
DA.wilWilcoxon Rank Sum and Signed Rank Test
DA.zigMetageonomeSeq ZIG
DA.znbZero inflated Negative Binomial glm
DA.zpoZero inflated Poisson glm
DA.zzzUser-defined function
featurePlotPlot association between abundance of a feature and predictor
groupSigAre some groups/taxa overrepresented among significant...
plot.DAPlotting results from 'testDA'
plot.DAPowerPlotting results from 'powerDA'
powerDAEstimating (empirical) statistical power
preDAPre-processing for DAtest
print.DAPrint results from 'testDA'
prune.tests.DAPrune tests argument for 'testDA'
runtimeDAEstimate runtime of 'testDA' on large datasets
spikeinSpike-in
summary.DASummary of results from 'testDA'
summary.DAPowerSummary of results from 'powerDA'
testDAComparing differential abundance/expression methods by FPR...
vennDAPlot Venn diagram from 'allDA' object
Russel88/DAtest documentation built on June 5, 2018, 8:21 p.m.