# Model-based Analysis of Single Cell Transcriptomics

## Documentation for package ‘MAST’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N P R S T U V W X Z misc

MAST-package | MAST: Model-based Analysis of Single- cell Transcriptomics

## -- A --

applyFlat | Apply a vectorized binary operation recycling over last dimension
assay-method | Default 'assay' returned

## -- B --

BayesGLMlike-class | Wrapper for bayesian GLM
bootVcov1 | Bootstrap a zlmfit
burdenOfFiltering | Filter a SingleCellAssay

## -- C --

calcZ | Get Z or T statistics and P values after running gseaAfterBoot
cData | Deprecated cell/feature data accessors/mutators
cData-method | Deprecated cell/feature data accessors/mutators
cData<- | Deprecated cell/feature data accessors/mutators
cData<--method | Deprecated cell/feature data accessors/mutators
coef-method | Wrapper for lmer/glmer
coef-method | An S4 class to hold the output of a call to zlm
CoefficientHypothesis | Describe a linear model hypothesis to be tested
colData<--method | Replace 'colData'
collectResiduals | Residual hooks and collection methods
combine-method | Deprecated cell/feature data accessors/mutators
combined_residuals_hook | Residual hooks and collection methods
computeEtFromCt | Compute the Et from the Ct
condmean | Summary statistics for genes in an experiment
condSd | Summary statistics for genes in an experiment
continuous_residuals_hook | Residual hooks and collection methods
convertMASTClassicToSingleCellAssay | Convert a MASTClassic SingleCellAssay
CovFromBoots | Extract the intere-gene covariance matrices for continuous and discrete components of a MAST model for a given coefficient from bootstrap replicates

## -- D --

defaultAssay | Default 'assay' returned
defaultPrior | Initialize a prior to be used a prior for BayeGLMlike/BayesGLMlike2
deviance_residuals_hook | Residual hooks and collection methods
discrete_residuals_hook | Residual hooks and collection methods
dof | Degrees of freedom of Zero inflated model
dof-method | Degrees of freedom of Zero inflated model
Drop | Drop specified dimension from an array

## -- E --

ebayes | Estimate hyperparameters for hierarchical variance model for continuous component
expavg | Exponential average

## -- F --

fData | fData
fData-method | fData
featureData | Accessor for featureData 'AnnotatedDataFrame'
featureData-method | Accessor for featureData 'AnnotatedDataFrame'
filter | Filter a SingleCellAssay
filterLowExpressedGenes | Filter low-expressing genes
fit | fit a zero-inflated regression
fit-method | fit a zero-inflated regression
fitted_phat | Residual hooks and collection methods
FluidigmAssay | Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table
freq | Summary statistics for genes in an experiment
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

## -- G --

getConcordance | Get the concordance between two experiments
getLogFC | Calculate log-fold changes from hurdle model components
getrc | Get the concordance between two experiments
getss | Get the concordance between two experiments
getwellKey | Accessor for wellKey
getwellKey-method | Accessor for wellKey
getwss | Get the concordance between two experiments
GLMlike-class | Wrapper for regular glm/lm
gseaAfterBoot | Gene set analysis for hurdle model
GSEATests-class | An S4 class for Gene Set Enrichment output
gsea_control | Gene set analysis for hurdle model

## -- H --

hushWarning | Selectively muffle warnings based on output
Hypothesis | Describe a linear model hypothesis to be tested

## -- I --

impute | impute missing continuous expression for plotting
influence.bayesglm | Influence bayesglm object
invlogit | Inverse of logistic transformation

## -- L --

LMERlike-class | Wrapper for lmer/glmer
LMlike-class | Linear Model-like Class
logFC | Calculate log-fold changes from hurdle model components
logLik-method | Wrapper for lmer/glmer
logLik-method | Linear Model-like Class
logmean | Log mean
LRT | Likelihood Ratio Tests for SingleCellAssays
LRT-method | Likelihood Ratio Tests for SingleCellAssays
lrTest | Run a likelihood-ratio test
lrTest-method | Linear Model-like Class
lrTest-method | An S4 class to hold the output of a call to zlm
lrTest-method | Likelihood ratio test

## -- M --

magic_assay_names | Default 'assay' returned
maits | MAITs data set, RNASeq
MAST | MAST: Model-based Analysis of Single- cell Transcriptomics
mast_filter | Filter a SingleCellAssay
melt.SingleCellAssay | "Melt" a 'SingleCellAssay' matrix
model.matrix | Model matrix accessor
model.matrix-method | Model matrix accessor
model.matrix<- | Replace model matrix
myBiplot | Makes a nice BiPlot

## -- N --

numexp | Summary statistics for genes in an experiment

## -- P --

partialScore | Residual hooks and collection methods
pbootVcov1 | Bootstrap a zlmfit
plot.thresholdSCRNACountMatrix | Plot cutpoints and densities for thresholding
plotlrt | Plot a likelihood ratio test object
plotSCAConcordance | Concordance plots of filtered single vs n-cell assays
predict.ZlmFit | Return predictions from a ZlmFit object.
predicted_sig | Predicted signatures
primerAverage | Average expression values for duplicated/redundant genes
print.summaryThresholdSCRNA | Summarize the effect of thresholding
print.summaryZlmFit | Print summary of a ZlmFit

## -- R --

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.

## -- S --

SceToSingleCellAssay | Coerce a SingleCellExperiment to some class defined in MAST
se.coef | Return coefficient standard errors
se.coef-method | An S4 class to hold the output of a call to zlm
show-method | show
SingleCellAssay | Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table
split-method | Split into 'list'
stat_ell | Plot confidence ellipse in 2D
subset-method | Subset a 'SingleCellAssay' by cells (columns)
summarize | Return programmatically useful summary of a fit
summary-method | Linear Model-like Class
summary-method | Summarize gene set enrichment tests
summary-method | Summarize model features from a 'ZlmFit' object
summary.thresholdSCRNACountMatrix | Summarize the effect of thresholding

## -- T --

thresholdSCRNACountMatrix | Threshold a count matrix using an adaptive threshold.

## -- U --

update-method | Wrapper for lmer/glmer
update-method | Linear Model-like Class

## -- V --

vbeta | Vbeta Data Set
vbetaFA | Vbeta Data Set, FluidigmAssay
vcov-method | Wrapper for regular glm/lm
vcov-method | Wrapper for lmer/glmer
vcov-method | An S4 class to hold the output of a call to zlm

## -- W --

waldTest | Run a Wald test
waldTest-method | Linear Model-like Class
waldTest-method | An S4 class to hold the output of a call to zlm
waldTest-method | Wald test

## -- X --

xform | Make matrix of continuous expression values, orthogonal to discrete

## -- Z --

zlm | Zero-inflated regression for SingleCellAssay
zlm.SingleCellAssay | Zero-inflated regression for SingleCellAssay
ZlmFit | An S4 class to hold the output of a call to zlm
ZlmFit-class | An S4 class to hold the output of a call to zlm

## -- misc --

"summary-ZlmFit", | Summarize model features from a 'ZlmFit' object
"ZlmFit-summary" | Summarize model features from a 'ZlmFit' object