Man pages for MAST
Model-based Analysis of Single Cell Transcriptomics

applyFlatApply a vectorized binary operation recycling over last...
BayesGLMlike-classWrapper for bayesian GLM
bootVcov1Bootstrap a zlmfit
calcZGet Z or T statistics and P values after running...
colData-set-SingleCellAssay-DataFrame-methodReplace 'colData'
collectResidualsResidual hooks and collection methods
computeEtFromCtCompute the Et from the Ct
convertMASTClassicToSingleCellAssayConvert a MASTClassic SingleCellAssay
CovFromBootsExtract the inter-gene covariance matrices for continuous and...
defaultAssayDefault 'assay' returned
defaultPriorInitialize a prior to be used a prior for...
dofDegrees of freedom of Zero inflated model
DropDrop specified dimension from an array
ebayesEstimate hyperparameters for hierarchical variance model for...
expavgExponential average
filterLowExpressedGenesFilter low-expressing genes
fitfit a zero-inflated regression
freqSummary statistics for genes in an experiment
FromFlatDFConstruct a SingleCellAssay (or derived subclass) from a...
FromMatrixConstruct a SingleCellAssay from a matrix or array of...
getConcordanceGet the concordance between two experiments
getwellKeyAccessor for wellKey
GLMlike-classWrapper for regular glm/lm
gseaAfterBootGene set analysis for hurdle model
GSEATests-classAn S4 class for Gene Set Enrichment output
hushWarningSelectively muffle warnings based on output
HypothesisDescribe a linear model hypothesis to be tested
imputeimpute missing continuous expression for plotting
influence.bayesglmInfluence bayesglm object
invlogitInverse of logistic transformation
LMERlike-classWrapper for lmer/glmer
LMlike-classLinear Model-like Class
logFCCalculate log-fold changes from hurdle model components
logmeanLog mean
LRTLikelihood Ratio Tests for SingleCellAssays
lrTestRun a likelihood-ratio test
lrTest-ZlmFit-character-methodLikelihood ratio test
maits-datasetMAITs data set, RNASeq
MAST-defunctDefunct functions in package 'MAST'
mast_filterFilter a SingleCellAssay
MAST-packageMAST: Model-based Analysis of Single- cell Transcriptomics
melt.SingleCellAssay"Melt" a 'SingleCellAssay' matrix
model.matrixModel matrix accessor
model.matrix-setReplace model matrix
myBiplotMakes a nice BiPlot
pbootVcov1Bootstrap a zlmfit
plotlrtPlot a likelihood ratio test object
plotSCAConcordanceConcordance plots of filtered single vs n-cell assays
plot.thresholdSCRNACountMatrixPlot cutpoints and densities for thresholding
predicted_sig-datasetPredicted signatures
predict.ZlmFitReturn predictions from a ZlmFit object.
primerAverageAverage expression values for duplicated/redundant genes
print.summaryZlmFitPrint summary of a ZlmFit
read.fluidigmReads a Fluidigm Biomark (c. 2011) raw data file (or set of...
removeResponseRemove the left hand side (response) from a formula
rstandard.bayesglmrstandard for bayesglm objects.
SceToSingleCellAssayCoerce a SingleCellExperiment to some class defined in MAST
se.coefReturn coefficient standard errors
split-SingleCellAssay-character-methodSplit into 'list'
stat_ellPlot confidence ellipse in 2D
subset-SingleCellAssay-methodSubset a 'SingleCellAssay' by cells (columns)
summarizeReturn programmatically useful summary of a fit
summary-GSEATests-methodSummarize gene set enrichment tests
summary.thresholdSCRNACountMatrixSummarize the effect of thresholding
summary-ZlmFit-methodSummarize model features from a 'ZlmFit' object
thresholdSCRNACountMatrixThreshold a count matrix using an adaptive threshold.
vbeta-datasetVbeta Data Set
vbetaFA-datasetVbeta Data Set, FluidigmAssay
waldTestRun a Wald test
waldTest-ZlmFit-matrix-methodWald test
xformMake matrix of continuous expression values, orthogonal to...
zlmZero-inflated regression for SingleCellAssay
ZlmFit-classAn S4 class to hold the output of a call to zlm
MAST documentation built on Nov. 8, 2020, 8:19 p.m.