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cyto_check()
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Check if input to cytoxxx function have errors |
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cytoflexmix()
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Logistic mixture regression |
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cytoglm()
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Fit GLM with bootstrap resampling |
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cytoglmm()
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Fit GLMM with method of moments |
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cytogroup()
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Group-specific fixed effects model |
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cytostab()
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Evaluate parameter stability with respect to gating sheme |
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generate_data()
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Generate dataset for vignettes and simulation studies |
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glmm_moment()
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Generalized linear mixed model with maximum likelihood |
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is_unpaired()
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Check if samples match or paired on condition |
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plot(<cytoflexmix>)
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Plot all components of mixture regression |
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plot(<cytoglm>)
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Plot bootstraped coefficients |
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plot(<cytoglmm>)
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Plot fixded coefficients of random effects model |
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plot(<cytogroup>)
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Plot fixded coefficients of group-specific fixed effects model |
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plot_coeff()
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Helper function to plot regression coeffcient |
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plot_heatmap()
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Heatmap of median marker expression |
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plot_lda()
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LDA on marker expression |
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plot_mds()
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MDS on median marker expression |
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plot_model_selection()
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Plot model selection to choose number optimal number of clusters |
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plot_prcomp()
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Plot PCA of subsampled data using ggplot |
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print(<cytoglm>)
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Extact and print bootstrap GLM fit |
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print(<cytoglmm>)
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Extact and print GLMM fit |
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remove_samples()
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Remove samples based on low cell counts |
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summary(<cytoglm>)
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Extact and calculate p-values of bootstrap GLM fit |
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summary(<cytoglmm>)
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Extact and calculate p-values of GLMM fit |