Functions to load data, add covariates or annotations, or provide high-level summaries.
Convert a MASTClassic SingleCellAssay
Summary statistics for genes in an experiment
Construct a SingleCellAssay (or derived subclass) from a `flat` (melted) data.frame/data.table
Construct a SingleCellAssay from a matrix or array of expression
Get the concordance between two experiments
Average expression values for duplicated/redundant genes
Reads a Fluidigm Biomark (c. 2011) raw data file (or set of files)
Zero-inflated regression for SingleCellAssay
Adaptive thresholding of background noise.
Plot cutpoints and densities for thresholding
Summarize the effect of thresholding
Threshold a count matrix using an adaptive threshold.
Fit a Hurdle linear model to test for zero-inflated differential expression.
Initialize a prior to be used a prior for BayeGLMlike/BayesGLMlike2
Estimate hyperparameters for hierarchical variance model for continuous component
Zero-inflated regression for SingleCellAssay
Testing linear functions of coefficients.
Describe a linear model hypothesis to be tested
Return coefficients, standard errors, etc. Calculate and return residuals from models.
Residual hooks and collection methods
collectResidualscombined_residuals_hookcontinuous_residuals_hookdeviance_residuals_hookdiscrete_residuals_hookfitted_phatpartialScoreimpute missing continuous expression for plotting
Calculate log-fold changes from hurdle model components
Return predictions from a ZlmFit object.
Return coefficient standard errors
An S4 class to hold the output of a call to zlm
ZlmFit-classcoef,ZlmFit-methodlrTest,ZlmFit,CoefficientHypothesis-methodlrTest,ZlmFit,Hypothesis-methodlrTest,ZlmFit,matrix-methodse.coef,ZlmFit-methodvcov,ZlmFit-methodwaldTest,ZlmFit,CoefficientHypothesis-methodwaldTest,ZlmFit,Hypothesis-methodTests on the average differential expression effect in a gene set, accounting for gene-gene correlations. Uses bootstraps to assess the gene-gene correlations.
Gene set analysis for hurdle model
Summarize gene set enrichment tests
Miscellaneous plotting methods. Concordance, PCA biplots, and effects plots for fitted hurdle models.