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LDAtopicmodel()
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Bayesian latent Dirichlet allocation for 16S and metagenomics data. |
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alignmentMatrix()
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aligned topics across chains |
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betaAligned()
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Align ASVs proportions in topics across chain. |
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dds_all_K_11
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'DESeqDataSet' object for the differential topic analysis on all samples in psE_BARBI.
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dds_all_paired_K_11
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'DESeqDataSet' object for the differential topic analysis on all paired-samples in psE_BARBI.
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dds_all_paired_aster_K_11
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'DESeqDataSet' object for the differential topic analysis on all Asteraceae paired-samples in psE_BARBI.
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dds_all_paired_nonaster_K_11
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'DESeqDataSet' object for the differential topic analysis on all non-Asteraceae paired-samples in psE_BARBI.
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diagnosticsPlot()
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Diagnostics plots - ESS and Rhat. |
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diffTop-package
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The 'diffTop' package. |
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diffTopAnalysis()
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Differential topic analysis |
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modelAssessment()
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Model assessment for LDA based on the maximum abundance for each taxon. |
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phyloseqTransformation()
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Anscombe (1948) transformation |
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plotASVCircular()
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Plot the ASVs distribution in each topic. |
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plotTopicProportion()
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Plot the topic distribution in all specimens. |
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powerstand
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A vector |
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powerswitch
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A vector |
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psE
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'phyloseq' object for the data published in Fitzpatrick et al. (2018).
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psE_BARBI
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'phyloseq' object for the data published in Fitzpatrick et al. (2018) after removing DNA contamination.
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ps_ans
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'phyloseq' object for the Anscombe transformed data published in Fitzpatrick et al. (2018) after removing DNA contamination.
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setUpData()
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Set-up data for latent Dirichlet allocation |
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thetaAligned()
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Align topic proportions in specimens across chain. |
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writeResTable()
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Write differential topic analysis results to latex |