BayesGLMlike-class      Wrapper for bayesian GLM
CovFromBoots            Extract the inter-gene covariance matrices for
                        continuous and discrete components of a MAST
                        model for a given coefficient from bootstrap
                        replicates
Drop                    Drop specified dimension from an array
FromFlatDF              Construct a SingleCellAssay (or derived
                        subclass) from a 'flat' (melted)
                        data.frame/data.table
FromMatrix              Construct a SingleCellAssay from a matrix or
                        array of expression
GLMlike-class           Wrapper for regular glm/lm
GSEATests-class         An S4 class for Gene Set Enrichment output
Hypothesis              Describe a linear model hypothesis to be tested
LMERlike-class          Wrapper for lmer/glmer
LMlike-class            Linear Model-like Class
LRT                     Likelihood Ratio Tests for SingleCellAssays
MAST-defunct            Defunct functions in package 'MAST'
MAST-package            MAST: Model-based Analysis of Single- cell
                        Transcriptomics
SceToSingleCellAssay    Coerce a SingleCellExperiment to some class
                        defined in MAST
ZlmFit-class            An S4 class to hold the output of a call to zlm
applyFlat               Apply a vectorized binary operation recycling
                        over last dimension
calcZ                   Get Z or T statistics and P values after
                        running gseaAfterBoot
colData<-,SingleCellAssay,DataFrame-method
                        Replace 'colData'
collectResiduals        Residual hooks and collection methods
computeEtFromCt         Compute the Et from the Ct
convertMASTClassicToSingleCellAssay
                        Convert a MASTClassic SingleCellAssay
defaultPrior            Initialize a prior to be used a prior for
                        BayeGLMlike/BayesGLMlike2
dof                     Degrees of freedom of Zero inflated model
ebayes                  Estimate hyperparameters for hierarchical
                        variance model for continuous component
expavg                  Exponential average
filterLowExpressedGenes
                        Filter low-expressing genes
fit                     fit a zero-inflated regression
freq                    Summary statistics for genes in an experiment
getConcordance          Get the concordance between two experiments
getwellKey              Accessor for wellKey
gseaAfterBoot           Gene set analysis for hurdle model
hushWarning             Selectively muffle warnings based on output
impute                  impute missing continuous expression for
                        plotting
influence.bayesglm      Influence bayesglm object
invlogit                Inverse of logistic transformation
logFC                   Calculate log-fold changes from hurdle model
                        components
logmean                 Log mean
lrTest                  Run a likelihood-ratio test
lrTest,ZlmFit,character-method
                        Likelihood ratio test
magic_assay_names       Default 'assay' returned
maits                   MAITs data set, RNASeq
mast_filter             Filter a SingleCellAssay
meld_list_left          Combine lists, preferentially taking elements
                        from x if there are duplicate names
melt.SingleCellAssay    "Melt" a 'SingleCellAssay' matrix
model.matrix            Model matrix accessor
model.matrix<-          Replace model matrix
myBiplot                Makes a nice BiPlot
new_with_repaired_slots
                        Instantiate a class, but warn rather than error
                        for badly named slots
pbootVcov1              Bootstrap a zlmfit
plot.thresholdSCRNACountMatrix
                        Plot cutpoints and densities for thresholding
plotSCAConcordance      Concordance plots of filtered single vs n-cell
                        assays
plotlrt                 Plot a likelihood ratio test object
predict.ZlmFit          Return predictions from a ZlmFit object.
predicted_sig           Predicted signatures
primerAverage           Average expression values for
                        duplicated/redundant genes
print.summaryZlmFit     Print summary of a ZlmFit
read.fluidigm           Reads a Fluidigm Biomark (c. 2011) raw data
                        file (or set of files)
removeResponse          Remove the left hand side (response) from a
                        formula
rstandard.bayesglm      rstandard for bayesglm objects.
se.coef                 Return coefficient standard errors
show,LMlike-method      show
split,SingleCellAssay,character-method
                        Split into 'list'
stat_ell                Plot confidence ellipse in 2D
subset,SingleCellAssay-method
                        Subset a 'SingleCellAssay' by cells (columns)
summarize               Return programmatically useful summary of a fit
summary,GSEATests-method
                        Summarize gene set enrichment tests
summary,ZlmFit-method   Summarize model features from a 'ZlmFit' object
summary.thresholdSCRNACountMatrix
                        Summarize the effect of thresholding
thresholdSCRNACountMatrix
                        Threshold a count matrix using an adaptive
                        threshold.
vbeta                   Vbeta Data Set
vbetaFA                 Vbeta Data Set, FluidigmAssay
waldTest                Run a Wald test
waldTest,ZlmFit,matrix-method
                        Wald test
xform                   Make matrix of continuous expression values,
                        orthogonal to discrete
zlm                     Zero-inflated regression for SingleCellAssay
